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Opened 6 years ago
Last modified 6 years ago
#3102 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.93 (2020-04-03)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.93 (2020-04-03)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/shirinmortazavi/Downloads/cryosparc_P22_J2141_007_volume_map_sharp_local.mrc
Opened cryosparc_P22_J2141_007_volume_map_sharp_local.mrc, grid size
256,256,256, pixel 1.23, shown at level 0.124, step 1, values float32
> ui mousemode rightMode zoom
> volume #1 level 0.8104
> volume #1 level 0.4071
> volume #1 level 0.3283
> volume #1 level 0.4395
> open2
> "/Users/shirinmortazavi/Downloads/cryosparc_P22_J2130_006_volume_map_sharp
> (1).mrc"
Opened cryosparc_P22_J2130_006_volume_map_sharp (1).mrc, grid size
384,384,384, pixel 0.818, shown at level 0.126, step 2, values float32
> volume #2 level 0.3427
> volume #2 step 1
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2051_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2051_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.17, step 1, values float32
> volume #3 level 0.5534
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2130_006_volume_map_sharp (1).mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 133933 points
correlation = 0.9509, correlation about mean = 0.6857, overlap = 6.739e+04
steps = 56, shift = 0.773, angle = 1.56 degrees
Position of cryosparc_P22_J2130_006_volume_map_sharp (1).mrc (#2) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99963010 0.02718969 -0.00061710 -4.14343340
-0.02719067 0.99962892 -0.00163723 4.76353371
0.00057235 0.00165340 0.99999847 0.40024337
Axis 0.06038652 -0.02182770 -0.99793638
Axis point 172.49617079 153.06286590 0.00000000
Rotation angle (degrees) 1.56129734
Shift along axis -0.75360192
> set bgColor white
> graphics silhouettes true
> set bgColor gray
> set bgColor gray
> set bgColor black
> set bgColor white
> volume #3 level 0.7846
> volume #2 level 0.5238
> volume #2 level 0.3751
> volume #2 level 0.346
> volume #2 level 0.2716
> volume #3 level 0.4855
> volume #2 level 0.2135
> volume #2 level 0.2846
> volume #3 level 0.3699
> toolshed show "Side View"
> volume #3 level 0.3087
> volume #3 level 0.2815
> open2 "/Users/shirinmortazavi/Documents/cryo-EM/CH's
> data/cryosparc_P22_J2136_006_volume_map_sharp_local.mrc"
Opened cryosparc_P22_J2136_006_volume_map_sharp_local.mrc, grid size
292,292,292, pixel 1.03, shown at level 0.276, step 2, values float32
> volume #4 step 1
> volume #4 level 0.3658
> select #4
3 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2018_008_volume_map_sharp_local.mrc
Opened cryosparc_P22_J2018_008_volume_map_sharp_local.mrc, grid size
256,256,256, pixel 1.23, shown at level 0.422, step 1, values float32
> volume #5 level 0.6006
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2136_006_volume_map_sharp_local.mrc in map
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc using 101160 points
correlation = 0.9751, correlation about mean = 0.6829, overlap = 3.926e+04
steps = 88, shift = 8.34, angle = 8.25 degrees
Position of cryosparc_P22_J2136_006_volume_map_sharp_local.mrc (#4) relative
to cryosparc_P22_J2018_008_volume_map_sharp_local.mrc (#5) coordinates:
Matrix rotation and translation
0.03854178 0.84419391 -0.53465053 105.27755894
-0.00374780 -0.53492219 -0.84489303 365.72350600
-0.99924997 0.03456744 -0.01745298 306.48365519
Axis 0.67287311 0.35546393 -0.64875818
Axis point 0.00000000 69.98187886 304.88314994
Rotation angle (degrees) 139.19312916
Shift along axis 2.00617405
> ui mousemode rightMode zoom
> volume #4 level 0.4017
> volume #4 level 0.2889
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2117_map_sharp.mrc
Opened cryosparc_P22_J2117_map_sharp.mrc, grid size 256,256,256, pixel 1.23,
shown at level 0.422, step 1, values float32
> volume #6 level 0.5641
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2117_map_sharp.mrc in map
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc using 62757 points
correlation = 0.99, correlation about mean = 0.8551, overlap = 4.367e+04
steps = 40, shift = 0.00576, angle = 0.00669 degrees
Position of cryosparc_P22_J2117_map_sharp.mrc (#6) relative to
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc (#5) coordinates:
Matrix rotation and translation
1.00000000 0.00007639 -0.00003823 -0.00915817
-0.00007639 0.99999999 -0.00007964 0.02138608
0.00003822 0.00007964 1.00000000 -0.01711682
Axis 0.68194223 -0.32731382 -0.65407986
Axis point 0.00000000 231.76332473 260.09197916
Rotation angle (degrees) 0.00669139
Shift along axis -0.00204954
Fit map cryosparc_P22_J2117_map_sharp.mrc in map
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc using 62757 points
correlation = 0.9901, correlation about mean = 0.8556, overlap = 4.363e+04
steps = 28, shift = 0.0267, angle = 0.0175 degrees
Position of cryosparc_P22_J2117_map_sharp.mrc (#6) relative to
cryosparc_P22_J2018_008_volume_map_sharp_local.mrc (#5) coordinates:
Matrix rotation and translation
0.99999996 0.00027314 -0.00002887 -0.03943950
-0.00027313 0.99999995 0.00015375 0.03888397
0.00002892 -0.00015375 0.99999999 0.02047535
Axis -0.48845621 -0.09179728 -0.86774639
Axis point 141.63904340 148.11936421 0.00000000
Rotation angle (degrees) 0.01803472
Shift along axis -0.00207238
> volume #4 level 0.3684
> open2 "/Users/shirinmortazavi/Documents/cryo-EM/CH's
> data/cryosparc_P22_J2143_map_sharp.mrc"
Opened cryosparc_P22_J2143_map_sharp.mrc, grid size 292,292,292, pixel 1.03,
shown at level 0.259, step 2, values float32
> volume #7 step 1
> volume #7 level 0.3239
> select #7
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> undo
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 99714 points
correlation = 0.9679, correlation about mean = 0.6508, overlap = 3.283e+04
steps = 92, shift = 5.24, angle = 11.3 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.00409633 0.53514700 0.84474902 -50.48993157
0.03590078 0.84429024 -0.53468227 106.09127097
-0.99934697 0.02813691 -0.02267069 308.30509650
Axis 0.28258824 0.92590989 -0.25066863
Axis point 111.32199244 0.00000000 194.32495755
Rotation angle (degrees) 95.23485495
Shift along axis 6.68067977
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 99714 points
correlation = 0.9679, correlation about mean = 0.6509, overlap = 3.283e+04
steps = 36, shift = 0.00517, angle = 0.0114 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
-0.00414088 0.53498756 0.84484979 -50.47195303
0.03585622 0.84439318 -0.53452268 106.06187693
-0.99934839 0.02807972 -0.02267916 308.31550848
Axis 0.28247875 0.92595907 -0.25061037
Axis point 111.34375734 -0.00000000 194.31269548
Rotation angle (degrees) 95.23341877
Shift along axis 6.68463831
> ui mousemode rightMode zoom
> volume #7 level 0.3347
> volume #6 level 0.5866
> volume #6 level 0.8001
> volume #6 color salmon
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
, dark slate blue
, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
, light blue
, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
, light seagreen
, light sky blue
, light skyblue
, light slate gray
, light slate grey
, light steel blue
, light yellow
, lightblue
, lightcoral
, lightcyan
, lightgoldenrodyellow
, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
, lime green
, limegreen
, linen
, magenta
, maroon
, medium aquamarine
, medium blue
, medium orchid
, medium purple
, medium sea green
, medium seagreen
, medium slate blue
, medium spring green
, medium turquoise
, medium violet red
, mediumaquamarine
, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
, pale goldenrod
, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
, skyblue
, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
.
> volume #7 color dodger blue
> volume #7 color sky blue
> volume #7 color deep sky blue
Expected a keyword
> volume #7 color dodger blue
> volume #7 color royal blue
> volume #7 color cornflower blue
> volume #7 color dodger blue
> ui mousemode rightMode "move planes"
> lighting simple
> lighting full
> lighting flat
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> volume #7 color royal blue
Expected a keyword
> volume #7 color steel blue
> volume #7 color royal blue
> volume #7 color cornflower blue
> volume #7 color dodger blue
> volume #7 color deep sky blue
> volume #7 color royal blue
> volume #7 color cornflower blue
> volume #7 color royal blue
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> ~select #7
Nothing selected
> hide #!7 models
> show #!7 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting full
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting simple
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting soft
> lighting flat
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting simple
> lighting shadows true
> lighting shadows false
> show #!6 models
> hide #!6 models
> volume #7 level 0.3024
> show #!6 models
> hide #!6 models
> volume #7 level 0.3588
> volume #6 region 0,0,0,255,255,255
> volume #6 region 0,0,0,255,255,255
> ui mousemode rightMode zoom
> volume #7 level 0.4488
> volume #6 level 0.8263
> volume #7 level 0.4166
> volume #6 level 0.8525
> volume #7 level 0.3373
> volume #7 level 0.3548
> volume #7 level 0.3481
> volume #6 level 0.7209
> ui mousemode rightMode "rotate selected models"
> select #7
4 models selected
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 79394 points
correlation = 0.9761, correlation about mean = 0.6534, overlap = 2.928e+04
steps = 60, shift = 3.31, angle = 2.84 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.03888261 0.84437801 -0.53433503 105.14478637
-0.00396457 -0.53460484 -0.84509287 365.74979344
-0.99923593 0.03497782 -0.01743924 306.46005063
Axis 0.67293951 0.35548301 -0.64867884
Axis point 0.00000000 69.98414577 304.87538260
Rotation angle (degrees) 139.16368307
Shift along axis 1.97976845
Fit map cryosparc_P22_J2143_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 79394 points
correlation = 0.9761, correlation about mean = 0.6535, overlap = 2.928e+04
steps = 28, shift = 0.021, angle = 0.0208 degrees
Position of cryosparc_P22_J2143_map_sharp.mrc (#7) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.03900481 0.84442765 -0.53424767 105.10287351
-0.00363417 -0.53453112 -0.84514099 365.68150390
-0.99923242 0.03490611 -0.01778049 306.52202599
Axis 0.67300801 0.35559286 -0.64854756
Axis point 0.00000000 69.96229298 304.82488286
Rotation angle (degrees) 139.17005056
Shift along axis 1.97469435
> ui mousemode rightMode zoom
> volume #6 level 0.5794
> volume #6 level 0.594
> volume #6 level 0.6916
> volume #6 level 0.7257
> volume #7 level 0.3376
> volume #7 level 0.3271
> volume #7 level 0.2974
> lighting simple
> lighting shadows true
> lighting shadows false
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> ~select #7
Nothing selected
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> save /Users/shirinmortazavi/Desktop/image10.png supersample 3
> show #!7 models
> volume #7 transparency 0.5
> volume #7 transparency 0.7
> save /Users/shirinmortazavi/Desktop/image11.png supersample 3
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0084_Ca2+andNS309/Cryosparc/cryosparc_P22_J1330_006_volume_map_sharp_local.mrc
Opened cryosparc_P22_J1330_006_volume_map_sharp_local.mrc, grid size
300,300,300, pixel 1.03, shown at level 0.466, step 2, values float32
> volume #8 step 1
> select #8
2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> volume #8 level 0.5862
> ui mousemode rightMode "rotate selected models"
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0084_Ca2+andNS309/cryosparc_P22_J2120_map_sharp.mrc
Opened cryosparc_P22_J2120_map_sharp.mrc, grid size 320,320,320, pixel 1.03,
shown at level 0.443, step 2, values float32
> volume #9 step 1
> volume #9 level 0.7195
> select #9
2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2120_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 68076 points
correlation = 0.9882, correlation about mean = 0.7825, overlap = 5.963e+04
steps = 76, shift = 4.02, angle = 7.38 degrees
Position of cryosparc_P22_J2120_map_sharp.mrc (#9) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.98624556 -0.16528567 -0.00060842 21.01183521
-0.16528590 -0.98622159 -0.00689565 349.12692320
0.00053972 0.00690137 -0.99997604 323.21520745
Axis 0.99655541 -0.08292963 -0.00001721
Axis point 0.00000000 174.87643246 162.21292102
Rotation angle (degrees) 179.60337512
Shift along axis -8.01906961
Fit map cryosparc_P22_J2120_map_sharp.mrc in map
cryosparc_P22_J2117_map_sharp.mrc using 68076 points
correlation = 0.9882, correlation about mean = 0.7825, overlap = 5.963e+04
steps = 24, shift = 0.01, angle = 0.0137 degrees
Position of cryosparc_P22_J2120_map_sharp.mrc (#9) relative to
cryosparc_P22_J2117_map_sharp.mrc (#6) coordinates:
Matrix rotation and translation
0.98626016 -0.16519817 -0.00069209 21.01481988
-0.16519889 -0.98623471 -0.00710133 349.15314058
0.00049056 0.00711809 -0.99997455 323.18808085
Axis 0.99655907 -0.08288560 -0.00005053
Axis point 0.00000000 174.87206643 162.21827999
Rotation angle (degrees) 179.59123347
Shift along axis -8.01358969
> select #9
3 models selected
> ~select #9
Nothing selected
> ui mousemode rightMode zoom
> volume #9 level 0.6832
> hide #!6 models
> hide #!6.1 models
> hide #!7 models
> show #!8 models
> hide #!8 models
> show #!6 models
> volume #9 level 0.5971
> color list
No custom colors.
248 builtin colors: alice blue
, aliceblue
, antique white
, antiquewhite
, aqua
, aquamarine
, azure
, beige
, bisque
, black
, blanched almond
, blanchedalmond
, blue
, blue violet
, blueviolet
, brown
, burly wood
, burlywood
, cadet blue
, cadetblue
, chartreuse
, chocolate
, coral
, cornflower blue
, cornflowerblue
, cornsilk
, crimson
, cyan
, dark blue
, dark cyan
, dark goldenrod
, dark gray
, dark green
, dark grey
, dark khaki
, dark magenta
, dark olive green
, dark orange
, dark orchid
, dark red
, dark salmon
, dark sea green
, dark seagreen
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, dark slate gray
, dark slate grey
, dark turquoise
, dark violet
, darkblue
, darkcyan
, darkgoldenrod
, darkgray
, darkgreen
, darkgrey
, darkkhaki
, darkmagenta
, darkolivegreen
, darkorange
, darkorchid
, darkred
, darksalmon
, darkseagreen
, darkslateblue
, darkslategray
, darkslategrey
, darkturquoise
, darkviolet
, deep pink
, deep sky blue
, deep skyblue
, deeppink
, deepskyblue
, dim gray
, dim grey
, dimgray
, dimgrey
, dodger blue
, dodgerblue
, fire brick
, firebrick
, floral white
, floralwhite
, forest green
, forestgreen
, fuchsia
, gainsboro
, ghost white
, ghostwhite
, gold
, goldenrod
, gray
, green
, green yellow
, greenyellow
, grey
, honeydew
, hot pink
, hotpink
, indian red
, indianred
, indigo
, ivory
, khaki
, lavender
, lavender blush
, lavenderblush
, lawn green
, lawngreen
, lemon chiffon
, lemonchiffon
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, light coral
, light cyan
, light goldenrod yellow
, light gray
, light green
, light grey
, light pink
, light salmon
, light sea green
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, light yellow
, lightblue
, lightcoral
, lightcyan
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, lightgray
, lightgreen
, lightgrey
, lightpink
, lightsalmon
, lightseagreen
, lightskyblue
, lightslategray
, lightslategrey
, lightsteelblue
, lightyellow
, lime
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, limegreen
, linen
, magenta
, maroon
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, medium spring green
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, medium violet red
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, mediumblue
, mediumorchid
, mediumpurple
, mediumseagreen
, mediumslateblue
, mediumspringgreen
, mediumturquoise
, mediumvioletred
, midnight blue
, midnightblue
, mint cream
, mintcream
, misty rose
, mistyrose
, moccasin
, navajo white
, navajowhite
, navy
, old lace
, oldlace
, olive
, olive drab
, olivedrab
, orange
, orange red
, orangered
, orchid
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, pale green
, pale turquoise
, pale violet red
, palegoldenrod
, palegreen
, paleturquoise
, palevioletred
, papaya whip
, papayawhip
, peach puff
, peachpuff
, peru
, pink
, plum
, powder blue
, powderblue
, purple
, rebecca purple
, rebeccapurple
, red
, rosy brown
, rosybrown
, royal blue
, royalblue
, saddle brown
, saddlebrown
, salmon
, sandy brown
, sandybrown
, sea green
, seagreen
, seashell
, sienna
, silver
, sky blue
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, slate blue
, slate gray
, slate grey
, slateblue
, slategray
, slategrey
, snow
, spring green
, springgreen
, steel blue
, steelblue
, tan
, teal
, thistle
, tomato
, transparent
, turquoise
, violet
, wheat
, white
, white smoke
, whitesmoke
, yellow
, yellow green
, and yellowgreen
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> volume #9 color #9190d4
> volume #9 color #9391d4
> volume #9 color #9591d4
> volume #9 color #9692d4
> volume #9 color #9792d4
> volume #9 color #9793d4
> volume #9 color #9893d4
> volume #9 color #9793d4
> volume #9 color #9693d4
> volume #9 color #9694d4
> volume #9 color #9695d4
> volume #9 color #9696d4
> volume #9 color #9797d4
> volume #9 color #9798d4
> volume #9 color #989ad4
> volume #9 color #989bd4
> volume #9 color #989cd4
> volume #9 color #979bd4
> volume #9 color #979ad4
> volume #9 color #979bd4
> volume #9 color #969ad4
> volume #9 color #9699d4
> volume #9 color #9599d4
> volume #9 color #9498d4
> volume #9 color #9397d4
> volume #9 color #9396d4
> volume #9 color #9295d4
> volume #9 color #9395d4
> volume #9 color #9293d4
> volume #9 color #8e8ed4
> volume #9 color #8f8fd4
> volume #9 color #8f90d4
> volume #9 color #9091d4
> volume #9 color #9192d4
> volume #9 color #9293d4
> volume #9 color #9294d4
> volume #9 color #9395d4
> volume #9 color #9396d4
> volume #9 color #9497d4
> volume #9 color #9598d4
> volume #9 color #9599d4
> volume #9 color #9499d4
> volume #9 color #9399d4
> volume #6 level 0.5648
> volume #6 level 0.5892
> volume #9 level 0.6561
> volume #9 level 0.6243
> volume #6 level 0.4867
> volume #6 level 0.5599
> volume #6 level 0.5989
> volume #6 level 0.716
> volume #6 level 0.716
> volume #6 level 0.7257
> volume #7 level 0.3096
> volume #9 level 0.8419
> volume #9 level 0.7059
> volume #9 level 0.7512
> volume #9 level 0.6878
> volume #6 level 0.6965
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> volume #7 transparency 0
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> volume #6 level 0.7989
> volume #6 level 0.7745
> save /Users/shirinmortazavi/Desktop/image9.png supersample 3
> save /Users/shirinmortazavi/Desktop/image10.png supersample 3
> save /Users/shirinmortazavi/Desktop/image11.png supersample 3
> volume #9 level 0.647
> save /Users/shirinmortazavi/Desktop/image12.png supersample 3
> volume #7 transparency 0.7
> volume #9 transparency 0.7
> volume #9 transparency 0
> volume #7 transparency 0
> volume #6 transparency 0.7
> save /Users/shirinmortazavi/Desktop/image13.png supersample 3
> save /Users/shirinmortazavi/Desktop/image14.png supersample 3
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> lighting shadows false
> graphics silhouettes true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> save /Users/shirinmortazavi/Desktop/image15.png supersample 3
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb" mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 6114
END
Chain information for Kv1.2-KCa31-TRAM-34_Wulff.pdb #10
---
Chain | Description
A B C D | No description available
> set bgColor black
> toolshed show "Side View"
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/TRAM34_dockingposition_in_Kv1.2.pdb
> close #10
> set bgColor white
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2051_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2051_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.17, step 1, values float32
> volume #2 level 0.4986
> volume #10 level 0.5825
> hide #!7 models
> close #8
> close #2
> close #4
> close #1
> close #7
> close #3
> ui mousemode rightMode pivot
> ui mousemode rightMode zoom
> toolshed show "Map Coordinates"
> molmap #11 4
> volume #1 color #ffff66
> volume #1 color #ffff0a
> volume #1 color #21ff06
> volume #1 color #66ff66
> volume #1 level 0.01452
> volume #10 level -0.9451
> volume #1 level 0
> volume #10 level 0.1614
> volume #10 level 0.2377
> select #1
4 models selected
> ui mousemode rightMode translate
> select #11
42 atoms, 45 bonds, 1 model selected
> select #1
4 models selected
> ui mousemode rightMode translate
> ui mousemode rightMode "translate selected models"
> volume #1 level 0.2952
> volume #1 level 0.3048
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> volume #10 level 1.276
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode translate
> ui mousemode rightMode rotate
> ui mousemode rightMode zoom
> volume #10 level 1.016
> select #11
42 atoms, 45 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> volume #10 level 0.6269
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ~select #11
Nothing selected
> ui mousemode rightMode zoom
> open 6cnn
6cnn title:
Cryo-EM structure of the human SK4/calmodulin channel complex in the Ca2+
bound state I [more info...]
Chain information for 6cnn #1
---
Chain | Description
A B C D | Intermediate conductance calcium-activated potassium channel protein
4
E F G H | Calmodulin-1
Non-standard residues in 6cnn #1
---
CA — calcium ion
K — potassium ion
LMT — dodecyl-β-D-maltoside
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)
> show cartoons
> hide atoms
> select #1
15740 atoms, 16004 bonds, 120 pseudobonds, 3 models selected
> ui mousemode rightMode rotate
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode translate
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> toolshed show "Fit in Map"
Fit molecule 6cnn (#1) to map cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) using 15740 atoms
average map value = 0.5517, steps = 92
shifted from previous position = 7.34
rotated from previous position = 11.4 degrees
atoms outside contour = 8931, contour level = 0.62692
Position of 6cnn (#1) relative to cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) coordinates:
Matrix rotation and translation
-0.00260445 0.99998876 -0.00395907 3.19825843
0.99998910 0.00258908 -0.00388288 2.99397884
-0.00387259 -0.00396914 -0.99998462 313.41629416
Axis -0.70618940 -0.70801730 0.00283433
Axis point 0.09924564 0.00000000 156.71415563
Rotation angle (degrees) 179.99650077
Shift along axis -3.49004125
Fit molecule 6cnn (#1) to map cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) using 15740 atoms
average map value = 0.5517, steps = 40
shifted from previous position = 0.00841
rotated from previous position = 0.0177 degrees
atoms outside contour = 8936, contour level = 0.62692
Position of 6cnn (#1) relative to cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) coordinates:
Matrix rotation and translation
-0.00251755 0.99998929 -0.00387866 3.16791249
0.99999039 0.00250360 -0.00359674 2.96305596
-0.00358699 -0.00388767 -0.99998600 313.35416659
Axis -0.70621733 -0.70799012 0.00266116
Axis point 0.08334543 0.00000000 156.68270257
Rotation angle (degrees) 179.98819803
Shift along axis -3.50116329
Fit molecule 6cnn (#1) to map cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) using 15740 atoms
average map value = 0.5517, steps = 48
shifted from previous position = 0.0205
rotated from previous position = 0.0206 degrees
atoms outside contour = 8932, contour level = 0.62692
Position of 6cnn (#1) relative to cryosparc_P22_J2051_006_volume_map_sharp.mrc
(#10) coordinates:
Matrix rotation and translation
-0.00248954 0.99998806 -0.00420148 3.22549746
0.99998989 0.00247378 -0.00375197 2.99865854
-0.00374153 -0.00421078 -0.99998413 313.41794072
Axis -0.70622679 -0.70798005 0.00282340
Axis point 0.08118154 0.00000000 156.71503480
Rotation angle (degrees) 179.98138875
Shift along axis -3.51601737
Missing or invalid "atoms" argument: invalid atoms specifier
> molmap #1 6
> ui mousemode rightMode zoom
> undo
> undo
> volume #2 level 0.4495
> hide #11 models
> show #11 models
> hide #11 models
> select #11
42 atoms, 45 bonds, 1 model selected
> show #11 models
> hide #!1 models
> hide #11 models
> show #11 models
> show #11 target m
> set bgColor black
> set bgColor white
> molmap #11 5
> volume #2 level 0.3272
> ~select #11
Nothing selected
> show #11 atoms
> color #11 byhetero
> color #11 byhetero
> molmap #11 6
> molmap #11 5
> molmap #11 6
> volume #2 level 0.07118
> toolshed show "Map Coordinates"
> volume #2 level 0.4781
> volume #2 level 0.3061
> volume #2 level 0.4288
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> lighting full
> lighting shadows false
> lighting simple
> graphics silhouettes false
> volume #2 level 0.2036
> volume #10 level 0.3507
> volume #10 level 0.3238
> volume #10 level 0.189
> volume #10 level 0.4383
> open2 /Users/shirinmortazavi/Documents/cryo-EM/SM0120_TRAM34/O1_T34.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-EM/SM0120_TRAM34/O1_T34.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 32467
Transform_accept_ratio 0.594
Ignored bad PDB record found on line 32468
if_X_angle_constraint 0
Ignored bad PDB record found on line 32469
if_X_atom_pair_constraint 0
Ignored bad PDB record found on line 32470
if_X_chainbreak 0
Ignored bad PDB record found on line 32471
if_X_coordinate_constraint 0
31 messages similar to the above omitted
Chain information for O1_T34.pdb #3
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #11#!3 atoms
> show #11#!3 cartoons
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ~select #3
Nothing selected
> ui mousemode rightMode zoom
> toolshed show "Fit in Map"
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 108
shifted from previous position = 10.1
rotated from previous position = 9.43 degrees
atoms outside contour = 18863, contour level = 0.43829
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00373250 0.99998421 -0.00419925 3.41400431
0.99998707 0.00371795 -0.00346681 2.75398645
-0.00345114 -0.00421214 -0.99998516 313.33347555
Axis -0.70579006 -0.70841590 0.00270441
Axis point 0.27672610 0.00000000 156.67216864
Rotation angle (degrees) 179.96974718
Shift along axis -3.51315529
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 48
shifted from previous position = 0.0197
rotated from previous position = 0.0145 degrees
atoms outside contour = 18865, contour level = 0.43829
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00396554 0.99998326 -0.00421307 3.45078661
0.99998582 0.00395052 -0.00356712 2.73240630
-0.00355042 -0.00422716 -0.99998475 313.37072137
Axis -0.70570805 -0.70849744 0.00274409
Axis point 0.31285671 0.00000000 156.69081268
Rotation angle (degrees) 179.97320569
Shift along axis -3.51123383
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 60
shifted from previous position = 0.0214
rotated from previous position = 0.0156 degrees
atoms outside contour = 18863, contour level = 0.43829
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00374264 0.99998418 -0.00419816 3.41437367
0.99998612 0.00372702 -0.00372077 2.78351849
-0.00370507 -0.00421203 -0.99998426 313.37143815
Axis -0.70578864 -0.70841697 0.00279115
Axis point 0.28210254 0.00000000 156.69131793
Rotation angle (degrees) 179.98005970
Shift along axis -3.50705021
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> volume #10 transparency 0.5
> volume #10 transparency 0.7
> volume #10 transparency 0.6
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/O1_T34_HB278.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-EM/SM0120_TRAM34/O1_T34_HB278.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 32467
Transform_accept_ratio 0.614
Ignored bad PDB record found on line 32468
if_X_angle_constraint 0
Ignored bad PDB record found on line 32469
if_X_atom_pair_constraint 0
Ignored bad PDB record found on line 32470
if_X_chainbreak 0
Ignored bad PDB record found on line 32471
if_X_coordinate_constraint 0
31 messages similar to the above omitted
Chain information for O1_T34_HB278.pdb #4
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #11#!3-4 atoms
> show #11#!3-4 cartoons
> select #4
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 120
shifted from previous position = 4.79
rotated from previous position = 5.96 degrees
atoms outside contour = 18853, contour level = 0.43829
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00399729 0.99998322 -0.00418927 3.44809573
0.99998556 0.00398220 -0.00360470 2.72823848
-0.00358795 -0.00420362 -0.99998472 313.37368798
Axis -0.70569115 -0.70851421 0.00275976
Axis point 0.31843990 0.00000000 156.69230373
Rotation angle (degrees) 179.97568632
Shift along axis -3.50145123
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 44
shifted from previous position = 0.012
rotated from previous position = 0.0213 degrees
atoms outside contour = 18850, contour level = 0.43829
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00379538 0.99998450 -0.00406891 3.40128458
0.99998527 0.00377955 -0.00389148 2.81201680
-0.00387605 -0.00408362 -0.99998414 313.39927313
Axis -0.70576068 -0.70844468 0.00282860
Axis point 0.28490638 0.00000000 156.70529483
Rotation angle (degrees) 179.99220103
Shift along axis -3.50617144
> hide #!3 models
> ~select #4
Nothing selected
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> hide #!10 models
> show #!10 models
> hide #11 models
> show #11 models
> hide #11 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/O1_T34_hb278_1to296_alignedto_6cnn_1to296.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/O1_T34_hb278_1to296_alignedto_6cnn_1to296.pdb" mode="rt"
encoding="utf-8">
---
warnings | Start residue of secondary structure not found: HELIX 51 51 GLU E 6
LEU E 18 1 13
Start residue of secondary structure not found: HELIX 52 52 THR E 29 SER E 38
1 10
Start residue of secondary structure not found: HELIX 53 53 GLU E 45 ASN E 53
1 9
Start residue of secondary structure not found: HELIX 54 54 PHE E 65 LYS E 75
1 11
Start residue of secondary structure not found: HELIX 55 55 GLU E 83 PHE E 92
1 10
35 messages similar to the above omitted
Chain information for O1_T34_hb278_1to296_alignedto_6cnn_1to296.pdb #7
---
Chain | Description
A B C D | No description available
> select #7
23494 atoms, 23733 bonds, 8 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> close #7
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/Kv1.2-KCa31-TRAM-34_Wulff.pdb" mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 6114
END
Chain information for Kv1.2-KCa31-TRAM-34_Wulff.pdb #7
---
Chain | Description
A B C D | No description available
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ~select #7
Nothing selected
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> hide #7 models
> show #7 models
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ~select #7
Nothing selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> hide #!10 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> toolshed show "Fit to Segments"
> select #4
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
Density map not found or not selected
Density map not found or not selected
> toolshed show "Fit in Map"
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 108
shifted from previous position = 2.09
rotated from previous position = 15 degrees
atoms outside contour = 3052, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93046748 0.36632247 -0.00617313 131.30923161
0.36635074 0.93046691 -0.00429511 90.96138457
0.00417050 -0.00625799 -0.99997171 318.19472016
Axis -0.18643919 -0.98246283 0.00268546
Axis point 56.59723434 0.00000000 159.36935116
Rotation angle (degrees) 179.69838592
Shift along axis -112.99286627
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 44
shifted from previous position = 0.0131
rotated from previous position = 0.0279 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93039635 0.36650596 -0.00600036 131.26038688
0.36653476 0.93039246 -0.00470374 91.04709437
0.00385874 -0.00657569 -0.99997093 318.21572653
Axis -0.18653619 -0.98244390 0.00287035
Axis point 56.57993447 0.00000000 159.38154583
Rotation angle (degrees) 179.71250895
Shift along axis -113.02008511
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.00532
rotated from previous position = 0.00833 degrees
atoms outside contour = 3051, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93040998 0.36646908 -0.00613647 131.28998575
0.36649892 0.93040641 -0.00473683 91.04878307
0.00397351 -0.00665620 -0.99996994 318.21928166
Axis -0.18651707 -0.98244744 0.00289924
Axis point 56.58513543 0.00000000 159.38828566
Rotation angle (degrees) 179.70519468
Shift along axis -113.01587234
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 60
shifted from previous position = 0.00756
rotated from previous position = 0.00592 degrees
atoms outside contour = 3047, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93039214 0.36651306 -0.00621482 131.30163669
0.36654322 0.93038920 -0.00468877 91.04639919
0.00406371 -0.00664040 -0.99996969 318.22396196
Axis -0.18654041 -0.98244306 0.00288300
Axis point 56.58310595 0.00000000 159.39228760
Rotation angle (degrees) 179.70027822
Shift along axis -113.02352313
> hide #7 models
> show #7 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #7 models
> show #7 models
> show #!3 models
> hide #7 models
> show #!4 models
> hide #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #7 models
> show #!10 models
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select ligand
434 atoms, 443 bonds, 4 models selected
Expected an objects specifier or a keyword
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel byhetero
> color sel bychain
> color sel byhetero
> select #7
6055 atoms, 6126 bonds, 1 model selected
> ~select #7
Nothing selected
> toolshed show "Fit in Map"
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 48
shifted from previous position = 0.0254
rotated from previous position = 0.035 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93020954 0.36697679 -0.00618308 131.26891174
0.36700529 0.93020875 -0.00433417 90.98490337
0.00416102 -0.00630091 -0.99997148 318.21967005
Axis -0.18678474 -0.98239714 0.00270650
Axis point 56.55815074 0.00000000 159.38274891
Rotation angle (degrees) 179.69835214
Shift along axis -113.04107596
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 48
shifted from previous position = 0.0055
rotated from previous position = 0.0128 degrees
atoms outside contour = 3048, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93025945 0.36685321 -0.00600446 131.24272482
0.36688066 0.93025782 -0.00435225 90.98459548
0.00398906 -0.00625164 -0.99997249 318.21381467
Axis -0.18671912 -0.98240963 0.00269854
Axis point 56.56271840 0.00000000 159.37442290
Rotation angle (degrees) 179.70857936
Shift along axis -113.03095734
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 48
shifted from previous position = 0.0211
rotated from previous position = 0.0431 degrees
atoms outside contour = 3053, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93046360 0.36632774 -0.00643951 131.35197701
0.36635689 0.93046530 -0.00411593 90.93190900
0.00448396 -0.00618888 -0.99997079 318.18812913
Axis -0.18644233 -0.98246241 0.00262228
Axis point 56.59735733 0.00000000 159.37143011
Rotation angle (degrees) 179.68147791
Shift along axis -112.99237162
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.00401
rotated from previous position = 0.02 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93045928 0.36634463 -0.00609329 131.29266348
0.36637181 0.93045927 -0.00415164 90.93492084
0.00414862 -0.00609534 -0.99997281 318.17974298
Axis -0.18645053 -0.98246089 0.00260757
Axis point 56.59514496 0.00000000 159.35674730
Rotation angle (degrees) 179.70135157
Shift along axis -112.98991334
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 60
shifted from previous position = 0.00615
rotated from previous position = 0.0159 degrees
atoms outside contour = 3051, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93040874 0.36646904 -0.00632496 131.32392496
0.36649731 0.93041018 -0.00407560 90.93166505
0.00439123 -0.00611005 -0.99997168 318.18057714
Axis -0.18651662 -0.98244839 0.00259200
Axis point 56.58834472 0.00000000 159.36324413
Rotation angle (degrees) 179.68751750
Shift along axis -113.00503936
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 60
shifted from previous position = 0.0216
rotated from previous position = 0.0327 degrees
atoms outside contour = 3043, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93028961 0.36677542 -0.00608370 131.26533458
0.36680385 0.93028754 -0.00447310 91.00548779
0.00401896 -0.00639280 -0.99997148 318.22192595
Axis -0.18667836 -0.98241719 0.00276519
Axis point 56.56947556 0.00000000 159.38318402
Rotation angle (degrees) 179.70539902
Shift along axis -113.02980947
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.0184
rotated from previous position = 0.0302 degrees
atoms outside contour = 3045, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93047737 0.36629837 -0.00611170 131.30116120
0.36632748 0.93047464 -0.00459518 91.01205272
0.00400358 -0.00651459 -0.99997076 318.21246242
Axis -0.18642671 -0.98246480 0.00282711
Axis point 56.59836325 0.00000000 159.38158235
Rotation angle (degrees) 179.70504507
Shift along axis -112.99455954
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 60
shifted from previous position = 0.0195
rotated from previous position = 0.0196 degrees
atoms outside contour = 3044, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93035431 0.36661183 -0.00605081 131.26846757
0.36664061 0.93035120 -0.00461429 91.02480731
0.00393773 -0.00651140 -0.99997104 318.23176108
Axis -0.18659209 -0.98243340 0.00283125
Axis point 56.57804513 0.00000000 159.38957348
Rotation angle (degrees) 179.70873155
Shift along axis -113.01847385
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.0208
rotated from previous position = 0.0246 degrees
atoms outside contour = 3051, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93048537 0.36627529 -0.00627451 131.32637108
0.36630532 0.93048353 -0.00456037 91.01062330
0.00416798 -0.00654175 -0.99996991 318.21388540
Axis -0.18641485 -0.98246706 0.00282516
Axis point 56.59817549 0.00000000 159.38690668
Rotation angle (degrees) 179.69550455
Shift along axis -112.99712144
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 76
shifted from previous position = 0.0183
rotated from previous position = 0.0206 degrees
atoms outside contour = 3044, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93036880 0.36657403 -0.00611199 131.28095716
0.36660307 0.93036616 -0.00457966 91.02002078
0.00400760 -0.00650145 -0.99997083 318.22894415
Axis -0.18657223 -0.98243720 0.00281990
Axis point 56.58030013 0.00000000 159.38952011
Rotation angle (degrees) 179.70491130
Shift along axis -113.01746161
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 64
shifted from previous position = 0.018
rotated from previous position = 0.0364 degrees
atoms outside contour = 3050, contour level = 0.43829
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93047597 0.36629720 -0.00638787 131.34631555
0.36632593 0.93047759 -0.00409196 90.93075670
0.00444490 -0.00614752 -0.99997122 318.18565209
Axis -0.18642606 -0.98246554 0.00260565
Axis point 56.59916614 0.00000000 159.36811791
Rotation angle (degrees) 179.68412371
Shift along axis -112.99363048
> volume #10 level 0.3086
> volume #10 level 0.2704
> volume #10 transparency 0.4
> volume #10 transparency 0.3
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> set bgColor black
> select #11
42 atoms, 45 bonds, 1 model selected
> show #11 models
> hide #7 models
> hide #!10 models
> show #!10 models
> show #7 models
> close #11
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/TRAM34_dockingposition_in_Kv1.2.pdb
> hide #7 models
> show #7 models
> set bgColor white
> set bgColor black
> volume #10 level 0.5528
> ui mousemode rightMode "translate selected models"
> select #8
42 atoms, 45 bonds, 1 model selected
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode zoom
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab
> select H
35792 atoms, 4 models selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select H
35792 atoms, 4 models selected
> hide sel target a
> select #8
42 atoms, 45 bonds, 1 model selected
> hide #8 models
> ~select #8
Nothing selected
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> select #7 /a,b,c,d:250
56 atoms, 52 bonds, 1 model selected
> color sel byhetero
> ~select #7 /a,b,c,d:250
Nothing selected
> volume #10 level 0.3849
Missing or invalid "filename" argument: Expected a file name
No help found for 'help:user/commands/open.htmlpubchem'
> open 679 pubchem
Missing filename suffix 679
> open 75151 pubchem
Missing filename suffix 75151
> open 75151 fromDatabase pubchem
Summary of feedback from opening 75151 fetched from pubchem
---
note | Fetching compressed PubChem 75151 from
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/75151/SDF?record_type=3d
PubChem entry 75151
> hide #7 models
> ui mousemode rightMode "translate selected models"
> select #11
10 atoms, 9 bonds, 1 model selected
> ~select #11
Nothing selected
> ui mousemode rightMode zoom
> select #11
10 atoms, 9 bonds, 1 model selected
> select H
35798 atoms, 5 models selected
> hide sel target a
> show #7 models
> ui mousemode rightMode "translate selected models"
> select #11
10 atoms, 9 bonds, 1 model selected
> ~select #11
Nothing selected
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> toolshed show "Fit in Map"
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5305, steps = 84
shifted from previous position = 0.00235
rotated from previous position = 0.0115 degrees
atoms outside contour = 2832, contour level = 0.38488
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93045997 0.36634087 -0.00621198 131.31556740
0.36636816 0.93046134 -0.00400717 90.91759804
0.00431202 -0.00600439 -0.99997267 318.17455490
Axis -0.18644862 -0.98246141 0.00254766
Axis point 56.59671562 0.00000000 159.35541483
Rotation angle (degrees) 179.69312590
Shift along axis -112.99603633
Fit molecule Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 6055 atoms
average map value = 0.5306, steps = 56
shifted from previous position = 0.016
rotated from previous position = 0.019 degrees
atoms outside contour = 2831, contour level = 0.38488
Position of Kv1.2-KCa31-TRAM-34_Wulff.pdb (#7) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.93036770 0.36657480 -0.00623252 131.30174447
0.36660313 0.93036784 -0.00422077 90.95824108
0.00425131 -0.00621172 -0.99997166 318.20518653
Axis -0.18657245 -0.98243762 0.00265484
Axis point 56.58158442 0.00000000 159.37513908
Rotation angle (degrees) 179.69429005
Shift along axis -113.01330171
> volume #10 level 0.2551
> volume #10 level 0.6138
> hide #11 models
> show #11 models
> hide #11 models
> show #11 models
> hide #11 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2142_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2142_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.163, step 1, values float32
> volume #12 level 0.7562
> volume #12 level 0.6661
> volume #10 level 0.6367
> volume #10 level 0.5451
> volume #10 level 0.652
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2142_006_volume_map_sharp.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 36785 points
correlation = 0.9951, correlation about mean = 0.9464, overlap = 4.432e+04
steps = 44, shift = 0.0238, angle = 0.0617 degrees
Position of cryosparc_P22_J2142_006_volume_map_sharp.mrc (#12) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99999945 0.00104664 -0.00009436 -0.16481899
-0.00104662 0.99999942 0.00023612 0.12215815
0.00009461 -0.00023602 0.99999997 0.04019466
Axis -0.21917592 -0.08772519 -0.97173361
Axis point 115.48470284 160.39383882 0.00000000
Rotation angle (degrees) 0.06171180
Shift along axis -0.01365050
Fit map cryosparc_P22_J2142_006_volume_map_sharp.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 36785 points
correlation = 0.9951, correlation about mean = 0.9463, overlap = 4.426e+04
steps = 40, shift = 0.0272, angle = 0.0168 degrees
Position of cryosparc_P22_J2142_006_volume_map_sharp.mrc (#12) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99999967 0.00080556 -0.00014088 -0.12152373
-0.00080550 0.99999960 0.00039785 0.08124985
0.00014120 -0.00039774 0.99999991 0.07325534
Axis -0.43742403 -0.15508838 -0.88578090
Axis point 96.10160723 164.10868689 0.00000000
Rotation angle (degrees) 0.05210487
Shift along axis -0.02433169
> hide #7 models
> volume #12 level 0.4107
> volume #12 level 0.7262
> volume #10 level 0.7283
> volume #12 level 0.4858
> volume #10 level 0.6596
> volume #10 level 0.4688
> lighting simple
> lighting shadows true
> lighting shadows false
> graphics silhouettes true
> set bgColor white
> set bgColor black
> volume #10 level 0.5985
> graphics silhouettes false
> graphics silhouettes true
> volume #10 level 0.4459
> graphics silhouettes false
> volume #10 level 0.4154
> graphics silhouettes true
> volume #10 level 0.4154
> graphics silhouettes false
> volume #10 level 0.4154
> graphics silhouettes true
> graphics silhouettes false
> volume #10 level 0.3925
> graphics silhouettes true
> graphics silhouettes false
> volume #10 level 0.423
> graphics silhouettes true
> volume #10 level 0.4383
> volume #10 level 0.4536
> volume #10 level 0.5451
> volume #10 level 0.5375
> volume #12 level 0.5835
> volume #12 level 0.4708
> volume #12 level 0.4708
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0120_TRAM34/DockInMap_14/placed_model.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0120_TRAM34/DockInMap_14/placed_model.pdb" mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 6065
Chain information for placed_model.pdb #13
---
Chain | Description
A B C D | No description available
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> preset "overall look" interactive
Preset expands to these ChimeraX commands:
~set bg
graphics silhouettes f
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting full
> lighting full
> lighting full
> lighting shadows false
> lighting shadows true
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> lighting flat
> lighting full
> set bgColor white
> set bgColor black
> set bgColor white
> set bgColor black
> lighting simple
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting simple
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> volume #10 level 0.2017
> volume #10 level 0.3391
> show #!4 models
> hide #!4 models
> show #!4 models
> toolshed show "Fit in Map"
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 64
shifted from previous position = 0.0229
rotated from previous position = 0.0269 degrees
atoms outside contour = 17053, contour level = 0.33909
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00356195 0.99998463 -0.00424610 3.39117534
0.99998749 0.00354700 -0.00352422 2.78838865
-0.00350910 -0.00425860 -0.99998476 313.34803499
Axis -0.70584552 -0.70836046 0.00275051
Axis point 0.24881144 0.00000000 156.67959919
Rotation angle (degrees) 179.97019394
Shift along axis -3.50696172
Fit molecule O1_T34_HB278.pdb (#4) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 48
shifted from previous position = 0.0198
rotated from previous position = 0.0164 degrees
atoms outside contour = 17063, contour level = 0.33909
Position of O1_T34_HB278.pdb (#4) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00380339 0.99998403 -0.00417686 3.41847866
0.99998611 0.00378810 -0.00366193 2.77462426
-0.00364605 -0.00419072 -0.99998456 313.37809900
Axis -0.70575971 -0.70844585 0.00277628
Axis point 0.28575740 0.00000000 156.69461074
Rotation angle (degrees) 179.97853548
Shift along axis -3.50827000
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 64
shifted from previous position = 0.024
rotated from previous position = 0.000536 degrees
atoms outside contour = 17067, contour level = 0.33909
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00374769 0.99998419 -0.00419028 3.41326140
0.99998610 0.00373211 -0.00372105 2.77930930
-0.00370536 -0.00420418 -0.99998429 313.39398090
Axis -0.70578695 -0.70841866 0.00278833
Axis point 0.28428441 0.00000000 156.70257368
Rotation angle (degrees) 179.98038984
Shift along axis -3.50410299
Fit molecule O1_T34.pdb (#3) to map
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) using 32414 atoms
average map value = 0.4193, steps = 64
shifted from previous position = 0.0234
rotated from previous position = 0.0152 degrees
atoms outside contour = 17057, contour level = 0.33909
Position of O1_T34.pdb (#3) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
-0.00363636 0.99998506 -0.00407937 3.38068224
0.99998728 0.00362206 -0.00350772 2.77253865
-0.00349290 -0.00409208 -0.99998552 313.32154539
Axis -0.70582527 -0.70838093 0.00267510
Axis point 0.26329833 0.00000000 156.66613950
Rotation angle (degrees) 179.97628231
Shift along axis -3.51201755
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> close #4
> close #3
> close #9
> close #6
> show #8 models
> hide #8 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> close #2
> open2 /Users/shirinmortazavi/Documents/cryo-EM/SM0121_TRAM34_2/O1_T34.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-EM/SM0121_TRAM34_2/O1_T34.pdb"
mode="rt" encoding="utf-8">
---
warnings | Ignored bad PDB record found on line 32467
Transform_accept_ratio 0.594
Ignored bad PDB record found on line 32468
if_X_angle_constraint 0
Ignored bad PDB record found on line 32469
if_X_atom_pair_constraint 0
Ignored bad PDB record found on line 32470
if_X_chainbreak 0
Ignored bad PDB record found on line 32471
if_X_coordinate_constraint 0
31 messages similar to the above omitted
Chain information for O1_T34.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> show #7,13#!2 cartoons
> hide #7,13#!2 atoms
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
434 atoms, 443 bonds, 4 models selected
> show sel target ab
> select H
22550 atoms, 5 models selected
> select #8
42 atoms, 45 bonds, 1 model selected
> select #7
6055 atoms, 6126 bonds, 1 model selected
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select H
22550 atoms, 5 models selected
> hide sel target a
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #2
Nothing selected
> hide #13 models
> show #13 models
> color #13#!2 byhetero
> select #13
6055 atoms, 6126 bonds, 1 model selected
> color sel byhetero
> select ligand
434 atoms, 443 bonds, 4 models selected
> color sel byhetero
> color sel bychain
> color sel byhetero
> undo
> undo
> select #13
6055 atoms, 6126 bonds, 1 model selected
> ~select #13
Nothing selected
> hide #!2 models
> volume #10 level 1.186
> volume #10 level 0.8351
> volume #10 level 0.6596
> volume #12 level 0.6886
> volume #10 level 0.6291
> close #1
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/DockInMap_15_O1_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_T34_rigid_in_2051_sharp.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0121_TRAM34_2/DockInMap_15_O1_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_T34_rigid_in_2051_sharp.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 32428
Chain information for placed_model_O1_KCa3.1_T34_rigid_in_2051_sharp.pdb #1
---
Chain | Description
A B C D | No description available
E F G H | No description available
> show #13#!1 cartoons
> hide #13#!1 atoms
> select #13
6055 atoms, 6126 bonds, 1 model selected
> hide #13 models
> close #13
> select #1
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
126 atoms, 135 bonds, 3 models selected
> show sel atoms
> select H
35798 atoms, 5 models selected
> hide sel target a
> select #1
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> select #1
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/DockInMap_16_O1_KCa3.1_TRAM34_HB278_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_TRAM34_HB278_rigid_in_2051_sharp.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0121_TRAM34_2/DockInMap_16_O1_KCa3.1_TRAM34_HB278_rigidbody_in_2051_sharp/placed_model_O1_KCa3.1_TRAM34_HB278_rigid_in_2051_sharp.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 32428
Chain information for
placed_model_O1_KCa3.1_TRAM34_HB278_rigid_in_2051_sharp.pdb #3
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #!1,3 atoms
> show #!1,3 cartoons
> close #2
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
126 atoms, 135 bonds, 3 models selected
> show sel target ab
> select N
6132 atoms, 4 bonds, 4 models selected
> select H
35798 atoms, 5 models selected
> hide sel target a
> select ligand
126 atoms, 135 bonds, 3 models selected
> color sel byhetero
> color sel byhetero
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color sel bychain
> undo
> color sel byhetero
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
126 atoms, 135 bonds, 3 models selected
> color sel byhetero
> color sel byhetero
> color sel byhetero
> select #3
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/DockInMap_17_O2_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O2_KCa3.1_TRAM34_rigid_in_2051_sharp.pdb
Summary of feedback from opening <_io.textiowrapper
name="/Users/shirinmortazavi/Documents/cryo-
EM/SM0121_TRAM34_2/DockInMap_17_O2_KCa3.1_TRAM34_rigidbody_in_2051_sharp/placed_model_O2_KCa3.1_TRAM34_rigid_in_2051_sharp.pdb"
mode="rt" encoding="utf-8">
---
warning | Ignored bad PDB record found on line 32428
Chain information for placed_model_O2_KCa3.1_TRAM34_rigid_in_2051_sharp.pdb #2
---
Chain | Description
A B C D | No description available
E F G H | No description available
> hide #!1-3 atoms
> show #!1-3 cartoons
> volume #10 level 1.14
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> select ligand
168 atoms, 180 bonds, 4 models selected
> show sel target ab
> select H
52139 atoms, 6 models selected
> hide sel target a
> color sel byhetero
> color sel byhetero
> select #2
32414 atoms, 32701 bonds, 8 pseudobonds, 2 models selected
> ~select #2
Nothing selected
> volume #10 level 0.8046
> hide #!2 models
> volume #10 level 1.041
> volume #10 level 0.8275
> volume #10 level 0.7054
> volume #10 level 0.5299
> hide #!3 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #10 level 0.3391
> show #11 models
> select #11
10 atoms, 9 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> volume #10 level 0.5604
> hide #!1 models
> hide #!3 models
> ui mousemode rightMode "translate selected atoms"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode zoom
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ~select #11
Nothing selected
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> ui mousemode rightMode "translate selected models"
> select #11
10 atoms, 9 bonds, 1 model selected
> volume #10 level 0.2933
> volume #12 level 0.4558
> volume #10 level 0.5375
> volume #10 level 0.5299
> volume #10 level 0.5451
> volume #10 level 0.5375
> volume #12 level 0.4483
> undo
> ~select #11
Nothing selected
> volume #12 level 0.4633
> volume #12 level 0.4934
> volume #12 level 0.4633
> ui mousemode rightMode zoom
> molmap #11 4
Expected a keyword
> molmap #11 4 cutoffRange 3
> molmap #11 4 cutoffRange 4
> molmap #11 4 cutoffRange 5
> molmap #11 4 cutoffRange 4
> molmap #11 4 cutoffRange 5
> molmap #11 4 cutoffRange 3
> molmap #11 4 cutoffRange 5
> molmap #11 4 onGrid #10
> volume #4 level 0.09668
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2145_map_locres.mrc
Opened cryosparc_P22_J2145_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 3.75, step 1, values float32
> volume #10 level 1.545
> volume #10 level 0.6062
> toolshed show "Fit in Map"
Fit map cryosparc_P22_J2145_map_locres.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 167735 points
correlation = 0.6639, correlation about mean = -0.0393, overlap = 3.006e+05
steps = 52, shift = 1.16, angle = 2.05 degrees
Position of cryosparc_P22_J2145_map_locres.mrc (#5) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99936584 0.03527935 0.00482592 -6.36493002
-0.03529546 0.99937149 0.00329524 5.19416258
-0.00470663 -0.00346349 0.99998293 2.43291390
Axis -0.09448056 0.13325580 -0.98656795
Axis point 148.02785744 186.03992728 0.00000000
Rotation angle (degrees) 2.04978343
Shift along axis -1.10672042
Fit map cryosparc_P22_J2145_map_locres.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 167735 points
correlation = 0.6639, correlation about mean = -0.03927, overlap = 3.006e+05
steps = 40, shift = 0.00471, angle = 0.00585 degrees
Position of cryosparc_P22_J2145_map_locres.mrc (#5) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99936549 0.03527564 0.00492368 -6.38291372
-0.03529195 0.99937171 0.00326601 5.20043371
-0.00480537 -0.00343771 0.99998255 2.44716833
Axis -0.09369299 0.13597591 -0.98627186
Axis point 148.30405178 186.55548370 0.00000000
Rotation angle (degrees) 2.05018917
Shift along axis -1.10840525
Fit map cryosparc_P22_J2145_map_locres.mrc in map
cryosparc_P22_J2051_006_volume_map_sharp.mrc using 167735 points
correlation = 0.664, correlation about mean = -0.03933, overlap = 3.006e+05
steps = 40, shift = 0.011, angle = 0.00374 degrees
Position of cryosparc_P22_J2145_map_locres.mrc (#5) relative to
cryosparc_P22_J2051_006_volume_map_sharp.mrc (#10) coordinates:
Matrix rotation and translation
0.99936411 0.03532047 0.00488301 -6.37519416
-0.03533676 0.99937005 0.00329035 5.20051206
-0.00476372 -0.00346080 0.99998266 2.43754587
Axis -0.09424828 0.13467147 -0.98639792
Axis point 148.05662576 186.10496414 0.00000000
Rotation angle (degrees) 2.05253217
Shift along axis -1.10317851
> volume #5 level 3.677
> volume #10 level 0.6749
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2051_006_volume_map_sharp.mrc
Opened cryosparc_P22_J2051_006_volume_map_sharp.mrc, grid size 256,256,256,
pixel 1.23, shown at level 0.17, step 1, values float32
> volume #6 level 0.5673
> volume #10 level 0.5909
> volume #10 level 0.5757
> volume #6 level 0.552
> volume #10 level 0.5222
> volume #10 level 0.8122
> hide #11 models
> volume #10 level 0.4536
> volume #10 level 0.5299
> volume #10 level 0.7206
> volume #10 level 0.8733
> toolshed show "Measure and Color Blobs"
> toolshed show Shell
Missing or invalid "surfaces" argument: empty atom specifier
Unknown command: local resolution
> color sample #10 map #5 palette rainbow
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> measure blob #!10.1 triangleNumber 42184 color #0000ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 5691
area = 6903.5
size = 65.763 49.34 30.353
> measure blob #!10.1 triangleNumber 36022 color #2de170ff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 6038.5
area = 7654.2
size = 53.454 46.664 46.829
> undo
> redo
> ui mousemode rightMode zoom
> hide #!10 models
> show #!10 models
> hide #!5 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> ui mousemode rightMode "pick blobs"
> measure blob #!10.1 triangleNumber 32222 color #0000ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 5691
area = 6903.5
size = 65.763 49.34 30.353
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> toolshed show "Measure and Color Blobs"
> color sample #10 map #5 palette rainbow
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> ui mousemode rightMode translate
> ui mousemode rightMode zoom
> toolshed show "Measure and Color Blobs"
> measure blob #!10.1 triangleNumber 69512 color #0000ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 463.47
area = 465.35
size = 22.95 13.622 7.2265
> measure blob #!10.1 triangleNumber 41359 color #0499ccff outline true
Surface cryosparc_P22_J2051_006_volume_map_sharp.mrc #10.1 blob:
volume = 30.687
area = 51.106
size = 4.2121 4.3764 3.6348
> color sample #10 map #5 palette rainbow
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> ui mousemode rightMode distance
> ui mousemode rightMode zoom
> toolshed show ViewDockX
No suitable models found for ViewDockX
> toolshed show "Show Volume Menu"
> toolshed show "Map Coordinates"
> toolshed show "Show Volume Menu"
> toolshed show "Volume Viewer"
> help help:devel
> help help:index.html
> color sample #10 map #5 palette rainbow range full
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> color sample #10 map #5 palette rainbow range full
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
Expected a keyword
Expected a keyword
Expected a keyword
> color sample #10 map #5 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> hide #!10 models
> show #!10 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2147_map_locres.mrc
> /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2148_map_locres.mrc
Opened cryosparc_P22_J2147_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 3.75, step 1, values float32
Opened cryosparc_P22_J2148_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 3.19, step 1, values float32
> color sample #10 map #5 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 1.144, mean 4.559, maximum 8.113
> volume #10 level 0.9343
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.441, maximum 8.05
> volume #9 level 5.914
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.441, maximum 8.05
> volume #9 level 3.499
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.441, maximum 8.05
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.458, maximum 6.769
> volume #13 level 2.929
> volume #10 level 0.8351
> volume #10 level 0.8656
> volume #13 level 2.652
> volume #10 level 0.4993
> volume #9 level 3.446
> volume #10 level 0.9801
> open2
> /Users/shirinmortazavi/Downloads/cryosparc_P22_J348_003_volume_map_sharp.mrc
Opened cryosparc_P22_J348_003_volume_map_sharp.mrc, grid size 286,286,286,
pixel 0.72, shown at level 0.0997, step 2, values float32
> volume #6 step 1
> volume #6 level 0.03806
> volume #6 level 0.03009
> volume #6 level 0.01681
> volume #6 level 0.02478
> volume #6 level 0.03965
> volume #6 level 0.03221
> volume #6 level 0.02478
> volume #6 level 0.03434
> volume #6 level 0.04284
> volume #6 level 0.06514
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2153_map_locres.mrc
Opened cryosparc_P22_J2153_map_locres.mrc, grid size 256,256,256, pixel 1.23,
shown at level 51.3, step 1, values float32
> volume #13 level 0.1539
> volume #6 level 46.11
> volume #13 level 3.398
> volume #6 level 48.35
> volume #6 level 51.88
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> volume #6 level 9.433
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> volume #6 level 2.056
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> volume #6 level 0
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> undo
> undo
> undo
> undo
> undo
> undo
> redo
> redo
> undo
> redo
> undo
> redo
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> color sample #10 map #6 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 2.666, mean 3.487, maximum 5.651
> undo
> undo
> redo
> undo
> redo
> volume #6 level 50.25
> volume #13 level 0
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
> undo
> redo
> undo
> undo
> redo
> redo
> undo
> redo
> redo
> redo
> undo
> redo
> volume #13 level 4.776
> color sample #10 map #9 palette 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 4.419, maximum 7.997
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
> volume #13 level 2.733
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
> undo
> undo
> redo
> undo
> redo
> color sample #10 map #13 palette
> 3,red:3.4,yellow:3.8,green:4.2,cyan:4.6,blue
Map values for surface "surface": minimum 0, mean 3.451, maximum 5.651
Map values for surface "cap near": minimum 0.438, mean 3.219, maximum 3.855
> set bgColor white
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting full
> lighting full
> lighting shadows false
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> lighting simple
> lighting full
> lighting flat
> lighting simple
> lighting full
> lighting shadows false
> lighting simple
> graphics silhouettes false
> lighting full
> lighting simple
> lighting shadows true
> lighting full
> lighting full
> lighting simple
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> volume #10 level 0.8759
Expected a keyword
> volume gaussian #10 bfactor -100
> volume #10 level 0.9131
> volume #14 level 1.329
> volume #14 level 1.374
> volume #14 level 1.171
> volume #10 level 0.6674
> volume gaussian #10 bfactor -200
> volume #15 level 14.44
> volume gaussian #10 bfactor -50
> volume #15 level 0.7736
> volume #15 level 0.9198
> volume #15 level 0.7493
> volume #10 level 0.4142
> volume #10 level 0.4366
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
> volume #12 level 0.4413
> volume gaussian #12 bfactor -50
> volume #5 level 0.509
> volume #5 level 0.6889
> volume #5 level 0.599
> volume #15 level 0.6884
> volume #5 level 0.7227
> volume #5 level 0.6664
> volume #5 level 0.6777
> volume #5 level 0.4303
> volume #15 level 0.5422
> volume #15 level 0.6884
> volume #5 level 0.5765
> volume #15 level 0.6518
> volume #15 level 0.7127
> volume #5 level 0.599
> volume #5 level 0.6327
> volume #15 level 0.6884
> volume gaussian #10 bfactor -100
> volume #9 level 0.8783
> volume #9 level 1.013
> volume #9 level 1.374
> volume #9 level 0.8558
> show #!4 models
> hide #!4 models
> show #!1 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> show #!3 models
> hide #!3 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #!10 models
> hide #!10 models
> hide #!9 models
> show #!9 models
> volume #9 level 1.599
> volume #9 level 1.104
> volume #9 level 0.9234
> volume #9 level 0.8333
> volume #9 level 0.9684
> volume #5 level 0.5765
> volume #9 level 0.9684
> volume #15 level 0.6884
> volume #15 level 0.7006
> volume #9 level 0.9909
> volume #9 level 1.013
> volume #9 level 1.036
> volume #9 level 1.059
> volume #15 level 0.7127
> volume #9 level 0.9459
> volume #15 level 0.4813
> volume #15 level 0.4326
> volume #15 level 0.6884
> volume #9 level 0.8783
> volume #9 level 0.9234
> volume #9 level 0.9008
> show #!4 models
> hide #!4 models
> show #!4 models
> volume gaussian #4 bfactor -100
> volume #13 level 2.882
> volume gaussian #4 bfactor -50
> volume #14 level 0.07733
> show #!4 models
> volume #15 level 0.6884
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #11 models
> hide #11 models
> open2 /Users/shirinmortazavi/Documents/cryo-
> EM/SM0121_TRAM34_2/cryosparc_P22_J2155_map_sharp.mrc
Opened cryosparc_P22_J2155_map_sharp.mrc, grid size 256,256,256, pixel 1.23,
shown at level 0.224, step 1, values float32
> volume #13 level 0.4386
> volume #13 level 0.616
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Window position QRect(689,1069 100x30) outside any known screen, using primary
screen
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 138, in _redraw_timer_callback
drew = self.draw_new_frame()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 62, in draw_new_frame
surface.update_clip_caps(view)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 30, in update_clip_caps
subdivision = settings.clipping_cap_subdivision)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 46, in show_surface_clip_caps
set_cap_drawing_geometry(d, p.name, varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/cap.py", line 184, in set_cap_drawing_geometry
cm.set_geometry(varray, narray, tarray)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/graphics/drawing.py", line 649, in set_geometry
arv()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 154, in <lambda>
arv = lambda self=self: self.set_vertex_colors(report_stats = False)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 229, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 199, in vertex_colors
values, outside = self.volume_values()
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 257, in volume_values
return self.offset_values(v, n, tf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 265, in offset_values
values, outside = self.vertex_values(v, xf)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/surface/colorvol.py", line 299, in vertex_values
out_of_bounds_list = True)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1334, in interpolated_values
subregion, step)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1510, in matrix_and_transform
m2s_transform = self.matrix_indices_to_xyz_transform(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1243, in
matrix_indices_to_xyz_transform
ijk_origin, ijk_size, ijk_step = self.ijk_aligned_region(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1297, in ijk_aligned_region
r = self.subregion(step, subregion)
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
AttributeError: 'NoneType' object has no attribute 'size'
AttributeError: 'NoneType' object has no attribute 'size'
File
"/Applications/ChimeraX-0.93.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 1558, in subregion
ijk_min, ijk_max = full_region(self.data.size)[:2]
See log for complete Python traceback.
OpenGL version: 4.1 INTEL-10.36.19
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.
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