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Opened 5 years ago
Last modified 2 years ago
#4551 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Tristan Croll | Owned by: | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-3.10.0-1127.19.1.el7.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103310726 (2021-03-31 07:26:37 UTC)
Description
View interpolation with the "fly" command causes weird shadow behaviour with "lighting soft".
Log:
UCSF ChimeraX version: 1.2.dev202103310726 (2021-03-31)
© 2016-2020 Regents of the University of California. All rights reserved.
> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/refinements/overview.cxs
> format session
Opened class4a_r_2.47A_postprocess_masked.mrc as #2, grid size 400,400,400,
pixel 0.999, shown at level 0.03, step 1, values float32
Opened class4a_r_2.47A_postprocess_masked.mrc as #3, grid size 400,400,400,
pixel 0.999, shown at level 0.018, step 1, values float32
Opened class4a_r_2.47A_postprocess_masked.mrc gaussian as #4, grid size
400,400,400, pixel 0.999, shown at level 0.0145, step 1, values float32
Log from Thu Apr 15 17:07:32 2021UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
> open overview.cxs
Log from Wed Apr 14 18:27:11 2021
> alias preview_toolshed toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu; toolshed reload available
> alias production_toolshed toolshed url https://cxtoolshed.rbvi.ucsf.edu;
> toolshed reload available
> alias st isolde step $*
> alias aw isolde add water $*
> alias awsf isolde add water sim false
> alias al isolde add ligand $*
> alias so setattr sel atoms occupancy $*
UCSF ChimeraX version: 1.1 (2020-09-09)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open model_1b_working_noh_real_space_refined.cif
Summary of feedback from opening model_1b_working_noh_real_space_refined.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 979
Missing entity information. Treating each chain as a separate entity.
Missing second residue in struct_conn "C00001"
Missing second residue in struct_conn "C00002"
Missing second residue in struct_conn "C00003"
Missing second residue in struct_conn "C00004"
Missing second residue in struct_conn "C00005"
20 messages similar to the above omitted
Missing first residue in struct_conn "C00026"
Missing second residue in struct_conn "C00027"
Missing first residue in struct_conn "C00028"
Missing first residue in struct_conn "C00029"
Missing second residue in struct_conn "C00030"
Missing second residue in struct_conn "C00031"
Missing second residue in struct_conn "C00032"
Missing first residue in struct_conn "C00033"
Missing second residue in struct_conn "C00034"
Missing second residue in struct_conn "C00035"
Missing second residue in struct_conn "C00036"
Missing second residue in struct_conn "C00037"
Missing second residue in struct_conn "C00038"
2 messages similar to the above omitted
Missing first residue in struct_conn "C00041"
Missing first residue in struct_conn "C00042"
Missing first residue in struct_conn "C00043"
Missing first residue in struct_conn "C00044"
Missing second residue in struct_conn "C00045"
Missing first residue in struct_conn "C00046"
Missing first residue in struct_conn "C00047"
Missing second residue in struct_conn "C00048"
Missing first residue in struct_conn "C00049"
Missing first residue in struct_conn "C00050"
Missing first residue in struct_conn "C00051"
Missing first residue in struct_conn "C00052"
Missing first residue in struct_conn "C00053"
18 messages similar to the above omitted
Missing second residue in struct_conn "C00072"
Missing second residue in struct_conn "C00073"
Missing second residue in struct_conn "C00074"
Missing second residue in struct_conn "C00075"
Missing second residue in struct_conn "C00076"
23 messages similar to the above omitted
Missing first residue in struct_conn "C00100"
Missing second residue in struct_conn "C00101"
Missing second residue in struct_conn "C00102"
Missing first residue in struct_conn "C00103"
Missing first residue in struct_conn "C00104"
Missing first residue in struct_conn "C00105"
Missing first residue in struct_conn "C00106"
Missing first residue in struct_conn "C00107"
1 messages similar to the above omitted
Invalid residue range for struct_conf "1": invalid entity "AA", near line 601
Invalid residue range for struct_conf "2": invalid entity "AA", near line 602
Invalid residue range for struct_conf "3": invalid entity "AA", near line 603
Invalid residue range for struct_conf "4": invalid entity "AB", near line 604
Invalid residue range for struct_conf "5": invalid entity "AB", near line 605
226 messages similar to the above omitted
Atom C1 is not in the residue template for GPC /AA:1007
Atom C1 is not in the residue template for GPC /AB:1005
Atom C1 is not in the residue template for GPC /AC:1005
Atom C1 is not in the residue template for GPC /AD:1007
Atom C1 is not in the residue template for GPC /AE:1007
19 messages similar to the above omitted
Atom C26 is not in the residue template for PEX /H1:1005
Atom C1 is not in the residue template for LMY /L:1019
Atom C26 is not in the residue template for PEX /M:1007
Atom C1 is not in the residue template for GPC /aa:1003
Atom C1 is not in the residue template for GPC /ab:1003
Atom C1 is not in the residue template for GPC /ac:1003
Atom C1 is not in the residue template for GPC /ad:1003
Atom C1 is not in the residue template for GPC /ae:1003
1 messages similar to the above omitted
Atom C26 is not in the residue template for PEX /af:1001
Atom C1 is not in the residue template for LMY /ag:1005
Atom C1 is not in the residue template for GPC /ag:1007
Atom C1 is not in the residue template for GPC /ah:1003
Atom C1 is not in the residue template for GPC /ai:1005
Atom C1 is not in the residue template for LMZ /ai:1001
7 messages similar to the above omitted
Atom C26 is not in the residue template for PEX /ba:1001
Atom C26 is not in the residue template for PEX /bb:1003
Atom C26 is not in the residue template for PEX /bc:1003
Atom C26 is not in the residue template for PEX /bd:1003
Atom C26 is not in the residue template for PEX /be:1003
12 messages similar to the above omitted
Atom C2A is not in the residue template for GUX /CG:2
Atom C2A is not in the residue template for GUX /MG:2
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 57678
Skipping chem_comp category: Missing column 'type' near line 58583
Skipping chem_comp category: Missing column 'type' near line 58981
Skipping chem_comp category: Missing column 'type' near line 59543
Skipping chem_comp category: Missing column 'type' near line 60102
13 messages similar to the above omitted
Chain information for model_1b_working_noh_real_space_refined.cif #1
---
Chain | Description
AA AB AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR AS AT AU AV AW AX | No
description available
AC AD | No description available
BA BC BF BG BH BJ BK BL BM BN BO BP BU BX ba bb bc bd be bf bg bh bi bj bk bl
bm bo bp | No description available
BB BD BE BI BQ BR BS BT BV BW bn | No description available
C | No description available
C1 | No description available
C2 | No description available
H1 | No description available
H2 | No description available
L | No description available
M | No description available
aa | No description available
ab ad ae af ag ah ai aj al am an ao | No description available
ac | No description available
ak ap | No description available
> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc
Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400, pixel
0.999, shown at level 0.0175, step 2, values float32
> volume #2 step 1
> surface dust #2
> volume #2 color #bf404000
> volume #2 color #ffffff10
> set bgColor white
> volume #2 color #bfb1b1
> volume #2 color #756d6d
> volume #2 color #757474
> volume #2 color #c4c1c1
> volume #2 color #c4c4c4
> volume #2 color #c8c8c8
> volume #2 color #252525
> volume #2 color #222222
> volume #2 color #1e1e1e
> volume #2 color #191919
> volume #2 color #171616
> volume #2 color #141414
> volume #2 color #171616
> volume #2 color #333131
> volume #2 color #333333
> volume #2 color #3a3a3a
> volume #2 color #404040
> volume #2 color #424242
> volume #2 color #4242425d
> volume #2 color #42424266
> volume #2 color #42424269
> volume #2 color #4242426a
> volume #2 color #4242427e
> volume #2 color #4242428c
> volume #2 color #4242428a
> volume #2 color #42424260
> volume #2 color #42424246
> volume #2 color #4242423e
> volume #2 color #4242423d
> volume #2 color #42424235
> volume #2 color #42424234
> volume #2 color #42424233
> volume #2 color #42424230
> volume #2 color #4242422f
> volume #2 color #4242422e
> volume #2 color #4242422c
> volume #2 color #42424223
> volume #2 color #42424221
> volume #2 color #42404021
> volume #2 color #e2dcdc21
> volume #2 color #e2e1e121
> volume #2 color #f7f6f621
> volume #2 color #f7f7f721
> volume #2 color #ffffff21
> volume #2 color #f4f4f421
> volume #2 color #f1f1f121
> volume #2 color #e1e1e121
> volume #2 color #cacaca21
> volume #2 color #b7b7b721
> volume #2 color #98989821
> volume #2 color #8e8e8e21
> volume #2 color #85858521
> volume #2 color #84848421
> volume #2 color #83838321
> volume #2 color #80808021
> volume #2 color #7a7a7a21
> volume #2 color #74747421
> volume #2 color #71717121
> volume #2 color #78787821
> volume #2 color #90909021
> volume #2 color #aaaaaa21
> volume #2 color #b0b0b021
> cartoon
> hide
> dssp
> select /C
2616 atoms, 2576 bonds, 16 pseudobonds, 422 residues, 2 models selected
> color /C green
> 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
.
> color /C lime
> color /M magenta
> color /L orange
> select /H1
721 atoms, 718 bonds, 84 residues, 1 model selected
> color /H1 cyan
> color /H2 lightseagreen
> select /S
Nothing selected
> color /C1 red
> color /C2 olivegreen
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color /C2 olive
> select /a*
9878 atoms, 10044 bonds, 64 pseudobonds, 1093 residues, 2 models selected
> volume #2 level 0.03183
> volume #2 level 0.03737
> color sel yellow
> color sel gold
> color sel yellow
> color /A* gold
> color /b*,B* cornflowerblue
> select clear
> select :GPC
1800 atoms, 1760 bonds, 40 residues, 1 model selected
> show
> hide protein
> hide
> select :GPC
1800 atoms, 1760 bonds, 40 residues, 1 model selected
> show sel
> color sel orangered
> select clear
> select :BCL
7128 atoms, 7560 bonds, 432 pseudobonds, 108 residues, 2 models selected
> show sel
> color sel blue
> select clear
> select :HEA,HEM,HEC
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> show sel
> color sel pink
> select clear
> volume #2 color #eeeeec
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC)
> select clear
> hide #!1 models
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
> hide #!2 models
> show #!1 models
> show :MAN,RAM,GUX,NDG
> color /C,CG lime
> color /M,MG magenta
> select :HEA,HEM,HEC
172 atoms, 184 bonds, 16 pseudobonds, 4 residues, 2 models selected
> color sel pink
> select clear
> show #!2 models
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
> select clear
> hide #!1 models
> select #1&~(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
6671 atoms, 6374 bonds, 566 residues, 1 model selected
> color sel white
> color zone #2 near #1&(protein|:BCL,HEM,HEC,GPC,MAN,RAM,GUX,NDG)
> open
> /run/media/tic20/storage/structure_dump/collaboration/pu_qian/2021_01_final_maps/model1b/class4a_r_2.47A_postprocess_masked.mrc
Opened class4a_r_2.47A_postprocess_masked.mrc, grid size 400,400,400, pixel
0.999, shown at level 0.0175, step 2, values float32
> volume #3 step 1
> volume #3 color #b0b0b021
> surface dust #3
> volume #3 level 0.01753
> volume #3 level 0.02399
> volume #3 level 0.01338
> volume #3 level 0.01707
> select clear
> volume #3 level 0.02122
> volume #3 level 0.01661
> volume #2 level 0.02952
> volume #3 level 0.01799
> surface dust #3
> volume gaussian #3 bfactor 80
> volume #4 color #b0b0b021
> volume #4 level 0.01281
> select clear
> volume #2 level 0.02574
> show #!1 models
> volume #2 level 0.02
> volume #2 level 0.03
> hide #!1 models
> lighting soft
> graphics silhouettes true
> graphics silhouettes false
> save overview.cxs
opened ChimeraX session
> hide #!4 models
> hide #!2 models
> show #!1 models
> show :CD4
> select :PEX
900 atoms, 880 bonds, 20 residues, 1 model selected
> select ~protein
15877 atoms, 15984 bonds, 448 pseudobonds, 726 residues, 8 models selected
> ui tool show Shell
/opt/UCSF/ChimeraX/lib/python3.7/site-packages/IPython/core/history.py:226:
UserWarning: IPython History requires SQLite, your history will not be saved
warn("IPython History requires SQLite, your history will not be saved")
> select /bi:21
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select :PGW
51 atoms, 50 bonds, 1 residue, 1 model selected
> show sel
> select :LMY
116 atoms, 118 bonds, 2 residues, 1 model selected
> show sel
> select :LMZ
55 atoms, 55 bonds, 1 residue, 1 model selected
> show sel
> select :CD4
504 atoms, 498 bonds, 6 residues, 1 model selected
> color sel green
> style sel sphere
Changed 504 atom styles
> select clear
> select /H1:1003@C05
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 1 bond, 4 residues, 1 model selected
> select clear
> select :PGW
51 atoms, 50 bonds, 1 residue, 1 model selected
> color sel tan
> style sel sphere
Changed 51 atom styles
> select clear
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
171 atoms, 173 bonds, 3 residues, 1 model selected
> color sel orange
> style sel sphere
Changed 171 atom styles
> select clear
> select :CDL
Nothing selected
> select :CD4
504 atoms, 498 bonds, 6 residues, 1 model selected
> select clear
> select :CD4,PGW,LMY,LMZ
726 atoms, 721 bonds, 10 residues, 1 model selected
> hide ~sel
> select clear
> cofr centerOfView showPivot true
> dssp
> ~cartoon /M
> cartoon /M
> select clear
> roll x 90
> roll x 90 1
> stop
> roll x 90 1
> ui mousemode right "mark point"
> marker #5 position 196.7,203,208.7 color yellow radius 1
> ui mousemode right "resize markers"
> marker change #5:1 radius 56.26
> ui mousemode right "move markers"
> marker change #5:1 position 199.8,200.8,208.8
> transparency sel 60
> transparency sel 60 target a
> marker change #5:1 position 200.3,200.9,208.8
> marker change #5:1 position 199.6,200.1,208.8
> ui mousemode right "resize markers"
> marker change #5:1 radius 56.26
> marker change #5:1 radius 57.4
> select clear
> ui mousemode right "move markers"
> marker change #5:1 position 199.8,199.4,208.8
> ui mousemode right "delete markers"
> show #!2 models
> show #!4 models
> hide #!1 models
> select clear
> color /M plum target s
> color /M plum
> color zone #2 near #1
> color /M,MG plum
> color zone #2 near #1
> volume #4 level 0.015
> volume #4 level 0.0145
> save overview.cxs
——— End of log from Thu Apr 15 17:07:32 2021 ———
opened ChimeraX session
> view name start
> show #!1 models
> hide #!2 models
> hide #!4 models
> view name p1
> view start
> view p1
> hide #!1 models
> show #!2 models
> show #!4 models
> fly 50 start p1
> fly 100 start p1
> view name p1
> view name p2
> fly 100 p1 p2
> usage fly
fly [namedViewOrFrames]
— interpolate camera and model motions for animations
namedViewOrFrames: a text string, repeatable
> fly 100 p1 p2
> lighting soft
> lighting full
> fly 100 p1 p2
> lighting soft
> fly 100 p1 p2
> lighting simple
> fly 100 p1 p2
> lighting soft
> hide #!4 models
> fly 100 p1 p2
> fly 100 p1 p2
> usage lighting
lighting [preset] [direction direction] [intensity a number] [color a color]
[fillDirection fillDirection] [fillIntensity a number] [fillColor a color]
[ambientIntensity a number] [ambientColor a color] [depthCue true or false]
[depthCueStart a number] [depthCueEnd a number] [depthCueColor a color]
[moveWithCamera true or false] [shadows true or false] [qualityOfShadows a
text string] [depthBias a number] [multiShadow an integer] [msMapSize an
integer] [msDepthBias a number]
— report or alter lighting parameters
preset: one of default, flat, full, gentle, simple, or soft
direction: some numbers
fillDirection: some numbers
lighting model models [depthCue true or false] [shadows true or false]
[multiShadow true or false] [directional true or false]
— Turn off depth cue or shadows for individual models even when globally they
are enabled.
> usage perframe
perframe command [ranges ranges] [frames an integer] [interval an integer]
[format a text string] [zeroPadWidth an integer] [showCommands true or false]
— Run a command before each graphics frame is drawn
command: a text string
ranges: a range, repeatable
perframe stop
— Stop all perframe commands
> perframe lighting soft
Expected a keyword
> perframe "lighting soft"
> fly 100 p1 p2
> perframe stop
> perframe "lighting soft" frames 100
> fly 100 p1 p2
> perframe stop
> fly 100 p1 p2
> movie record
> fly 200 p1 p2
> movie stop
> movie encode /home/tic20/Desktop/weird_lighting_during_fly.mp4
Movie saved to /home/tic20/Desktop/weird_lighting_during_fly.mp4
> lighting directional false
Expected one of 'default', 'flat', 'full', 'gentle', 'simple', or 'soft' or a
keyword
> lighting model #2 directional false
> lighting model #2 directional true
> lighting moveWithCamera false
> fly 200 p1 p2
> lighting moveWithCamera true
> fly 200 p1 p2
OpenGL version: 3.3.0 NVIDIA 455.32.00
OpenGL renderer: TITAN Xp/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Precision T5600
OS: CentOS Linux 7 Core
Architecture: 64bit ELF
Virutal Machine: none
CPU: 32 Intel(R) Xeon(R) CPU E5-2687W 0 @ 3.10GHz
Cache Size: 20480 KB
Memory:
total used free shared buff/cache available
Mem: 62G 4.0G 46G 83M 11G 58G
Swap: 4.9G 0B 4.9G
Graphics:
03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [TITAN Xp] [10de:1b02] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:11df]
Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.12.5
cftime: 1.4.1
chardet: 3.0.4
ChimeraX-AddCharge: 1.0
ChimeraX-AddH: 2.1.4
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.12
ChimeraX-AtomicLibrary: 3.0
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.5.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.1
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-Clipper: 0.15.0
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.2.1
ChimeraX-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202103310726
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.1
ChimeraX-DevelExtras: 0.4.0
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.0
ChimeraX-Hbonds: 2.1
ChimeraX-Help: 1.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.2.dev37
ChimeraX-Label: 1.0
ChimeraX-LinuxSupport: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.0.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.0
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 1.1
ChimeraX-MDcrds: 2.2
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.3
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.5
ChimeraX-PDB: 2.4
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PDBMatrices: 1.0
ChimeraX-Phenix: 0.2
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-ReadPbonds: 1.0
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.4
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.0
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.0.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.3
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0.1
ChimeraX-ToolshedUtils: 1.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.7.1
ChimeraX-uniprot: 2.1
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.3
comtypes: 1.1.7
cxservices: 1.0
cycler: 0.10.0
Cython: 0.29.21
decorator: 4.4.2
distlib: 0.3.1
distro: 1.5.0
docutils: 0.16
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 2.10.0
html2text: 2020.1.16
idna: 2.10
ihm: 0.17
imagecodecs: 2020.5.30
imagesize: 1.2.0
ipykernel: 5.3.4
ipython: 7.18.1
ipython-genutils: 0.2.0
jedi: 0.17.2
Jinja2: 2.11.2
jupyter-client: 6.1.7
jupyter-core: 4.7.1
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.6.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
networkx: 2.5
numexpr: 2.7.3
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.9
ParmEd: 3.2.0
parso: 0.7.1
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 21.0.1
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.18
psutil: 5.7.2
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.0.0
Pygments: 2.7.1
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.1
pytz: 2021.1
pyzmq: 22.0.3
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.2
sfftk-rw: 0.6.7.dev1
six: 1.15.0
snowballstemmer: 2.1.0
sortedcontainers: 2.2.2
Sphinx: 3.2.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 1.0.3
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.4
suds-jurko: 0.6
tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.36.0
wheel-filename: 1.2.0
File attachment: weird_lighting_during_fly.mp4
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