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Opened 2 hours ago
#20424 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.5-arm64-arm-64bit
ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.11.1 (2026-01-23)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/tomforan/Library/CloudStorage/OneDrive-
> Birkbeck,UniversityofLondon/modelling/2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb
> format pdb
Chain information for 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb #1
---
Chain | Description
A B | No description available
C F H a | No description available
D | No description available
E G M b | No description available
> cd
> /Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J290_map_sharp_all_classes_sharp/
Current working directory is:
/Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J290_map_sharp_all_classes_sharp
> open *.mrc vseries true
Opened map series J290_volume_class_00_map_sharp.mrc as #2, 20 images, grid
size 180,180,180, pixel 1.66, shown at level 0.234, step 1, values float32
> ui tool show "Fit in Map"
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J290_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.07496, steps = 180
shifted from previous position = 37.8
rotated from previous position = 0.183 degrees
atoms outside contour = 64361, contour level = 0.23397
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J290_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99999528 0.00241246 -0.00190198 29.01398635
-0.00241409 0.99999672 -0.00085453 -23.60032147
0.00189991 0.00085912 0.99999783 2.63445825
Axis 0.26865575 -0.59603790 -0.75667887
Axis point -4857.31806057 -9823.67011246 0.00000000
Rotation angle (degrees) 0.18273391
Shift along axis 19.86802144
> ui mousemode right "translate selected models"
> select add #2
22 models selected
> view matrix models #2,1,0,0,5.9383,0,1,0,10.907,0,0,1,17.491
> undo
> select add #1
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 25 models selected
> select subtract #2
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 3 models selected
> view matrix models
> #1,1,0.0024125,-0.001902,58.232,-0.0024141,1,-0.00085453,20.362,0.0018999,0.00085912,1,43.838
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J290_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.1103, steps = 164
shifted from previous position = 24.3
rotated from previous position = 27.7 degrees
atoms outside contour = 57262, contour level = 0.23397
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J290_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.88456862 0.46640640 -0.00185352 0.69049043
-0.46640664 0.88457037 0.00032648 85.29480865
0.00179184 0.00057570 0.99999823 52.74037267
Axis 0.00026717 -0.00390790 -0.99999233
Axis point 172.25495990 41.12070230 0.00000000
Rotation angle (degrees) 27.80151932
Shift along axis -53.07310700
> volume #2.1 level 0.1406
> select clear
> volume #2.1 level 0.07543
> volume #2.2 color #b2b2b299
Drag select of 2.5 J290_volume_class_04_map_sharp.mrc , 22 atoms
> select clear
> select /D:236@CG2
1 atom, 1 residue, 1 model selected
> select add /A:73@CG
2 atoms, 2 residues, 1 model selected
> select add /B:64@OD1
3 atoms, 3 residues, 1 model selected
> select up
43 atoms, 40 bonds, 3 residues, 1 model selected
> select up
242 atoms, 242 bonds, 14 residues, 1 model selected
> select up
15561 atoms, 15684 bonds, 992 residues, 1 model selected
> molmap sel 12 onGrid #2.4
Opened 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb map 12 as #3, grid size
180,180,180, pixel 1.66, shown at level 0.0483, step 1, values float32
> save "/Users/tomforan/OneDrive - Birkbeck, University of
> London/references/2DC+linker_2Kif_P501_J290.mrc" models #3
> close #2
> cd
> /Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J298_map_sharp_all_classes_sharp/
Current working directory is:
/Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J298_map_sharp_all_classes_sharp
> open *.mrc vseries true
Opened map series J298_volume_class_00_map_sharp.mrc as #2, 20 images, grid
size 180,180,180, pixel 1.66, shown at level 0.243, step 1, values float32
> volume #2.1 level 0.118
> hide #!3 models
> color #2 #b2ffff98 models
> color #2 #f4fef697 models
> select clear
> hide atoms
> show cartoons
> ui tool show "Hide Dust"
> volume #2.6 level 0.09208
> volume #2.6 level 0.1163
> select add #1
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 3 models selected
> view sel
> select clear
> select add #1
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 3 models selected
> ui tool show "Surface Zone"
> surface zone #3 nearAtoms #1 distance 9.94
> surface zone #2.1 nearAtoms #1 distance 9.94
> close #2
> open *.mrc vseries true
Opened map series J298_volume_class_00_map_sharp.mrc as #2, 20 images, grid
size 180,180,180, pixel 1.66, shown at level 0.243, step 1, values float32
> volume #2.1 level 0.1591
> surface dust #3 size 9.94
> volume #2.5 level 0.103
> volume #2.5 level 0.1505
> volume #2.7 level 0.1521
> volume #2.9 level 0.1381
> close #2
> cd
> /Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J302_map_sharp_all_classes_sharp/
Current working directory is:
/Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J302_map_sharp_all_classes_sharp
> open *.mrc vseries true
Opened map series J302_volume_class_00_map_sharp.mrc as #2, 5 images, grid
size 180,180,180, pixel 3.31, shown at level 0.669, step 1, values float32
> volume #2.1 level 0.2329
> ui tool show "Side View"
> volume #2.1 level 0.1015
> volume #2.1 level 0.028
> view matrix models
> #1,0.88457,0.46641,-0.0018535,25.235,-0.46641,0.88457,0.00032648,234.78,0.0017918,0.0005757,1,60.148
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4703, steps = 100
shifted from previous position = 34.8
rotated from previous position = 28.7 degrees
atoms outside contour = 4788, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99984956 -0.01629828 0.00593447 94.71027491
0.01631940 0.99986061 -0.00352660 183.92275185
-0.00587617 0.00362292 0.99997617 76.39445162
Axis 0.20185451 0.33345311 0.92090378
Axis point -8154.59793709 4018.67593995 0.00000000
Rotation angle (degrees) 1.01473853
Shift along axis 150.79924962
> view matrix models
> #1,0.99985,-0.016298,0.0059345,97.813,0.016319,0.99986,-0.0035266,183.11,-0.0058762,0.0036229,0.99998,191.89
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4918, steps = 68
shifted from previous position = 7.33
rotated from previous position = 0.157 degrees
atoms outside contour = 4887, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99988384 -0.01368349 0.00671388 94.31097644
0.01370842 0.99989926 -0.00368107 184.29222468
-0.00666283 0.00377268 0.99997069 198.50466162
Axis 0.23751872 0.42625842 0.87286231
Axis point -4900.85384983 2173.93054781 0.00000000
Rotation angle (degrees) 0.89905639
Shift along axis 274.22397323
> view matrix models
> #1,0.99988,-0.013683,0.0067139,91.714,0.013708,0.9999,-0.0036811,185.69,-0.0066628,0.0037727,0.99997,154.63
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4892, steps = 56
shifted from previous position = 4.29
rotated from previous position = 0.0539 degrees
atoms outside contour = 5033, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.99987635 -0.01445787 0.00618471 94.51907263
0.01448029 0.99988869 -0.00359590 184.20426506
-0.00613203 0.00368501 0.99997441 157.63561467
Axis 0.22554027 0.38153536 0.89641640
Axis point -6561.54497111 2960.38321540 0.00000000
Rotation angle (degrees) 0.92485284
Shift along axis 232.90544699
> volume #2.2 color #ffb2ff96
> volume #2.2 level 0.6847
> view matrix models
> #1,0.99988,-0.014458,0.0061847,265.48,0.01448,0.99989,-0.0035959,83.735,-0.006132,0.003685,0.99997,147.06
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4196, steps = 160
shifted from previous position = 59.7
rotated from previous position = 43.1 degrees
atoms outside contour = 7901, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.74072230 0.67180540 0.00282463 251.32460407
-0.67120066 0.74022167 -0.03951656 225.35593865
-0.02863829 0.02737491 0.99921492 154.57630564
Axis 0.04973199 0.02339182 -0.99848863
Axis point 425.63573832 -219.94280029 0.00000000
Rotation angle (degrees) 42.26181666
Shift along axis -136.57232370
> view matrix models
> #1,0.74072,0.67181,0.0028246,189.95,-0.6712,0.74022,-0.039517,171.75,-0.028638,0.027375,0.99921,242.39
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.385, steps = 128
shifted from previous position = 31.3
rotated from previous position = 31.7 degrees
atoms outside contour = 9696, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.27773698 0.96061461 -0.00904073 227.10943623
-0.96036349 0.27740710 -0.02733614 264.85484598
-0.02375154 0.01627464 0.99958541 246.19725283
Axis 0.02269587 0.00765578 -0.99971310
Axis point 293.68241604 -21.25362389 0.00000000
Rotation angle (degrees) 73.89701255
Shift along axis -238.94450183
> view matrix models
> #1,0.27774,0.96061,-0.0090407,173.97,-0.96036,0.27741,-0.027336,244.8,-0.023752,0.016275,0.99959,244.98
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.3401, steps = 116
shifted from previous position = 12.4
rotated from previous position = 27.2 degrees
atoms outside contour = 10853, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
-0.19243661 0.98099577 -0.02480808 216.93907723
-0.98093425 -0.19300055 -0.02277705 302.81973578
-0.02713217 0.01995196 0.99943272 254.60356211
Axis 0.02177389 0.00118431 -0.99976222
Axis point 235.92197056 60.09321156 0.00000000
Rotation angle (degrees) 101.12804242
Shift along axis -249.46078199
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.094606,-0.99225,-0.080497,405.57,0.97502,0.10868,-0.19372,125.22,0.20097,-0.060159,0.97775,246.16
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.3996, steps = 88
shifted from previous position = 26.2
rotated from previous position = 12.4 degrees
atoms outside contour = 7173, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.10866699 -0.99407400 0.00290134 386.96841389
0.99406704 0.10867916 0.00442812 81.33142087
-0.00471719 0.00240294 0.99998601 251.74439322
Axis -0.00101862 0.00383195 0.99999214
Axis point 148.79656542 256.11521752 0.00000000
Rotation angle (degrees) 83.76157346
Shift along axis 251.65989762
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.10867,-0.99407,0.0029013,392.41,0.99407,0.10868,0.0044281,78.146,-0.0047172,0.0024029,0.99999,218.78
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J302_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4209, steps = 72
shifted from previous position = 10.2
rotated from previous position = 0.115 degrees
atoms outside contour = 3995, contour level = 0.028
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J302_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.10701149 -0.99425341 0.00295689 387.12767570
0.99425120 0.10702116 0.00332575 81.67335672
-0.00362308 0.00258400 0.99999012 210.72539971
Axis -0.00037302 0.00330899 0.99999446
Axis point 148.52354887 256.04791513 0.00000000
Rotation angle (degrees) 83.85693665
Shift along axis 210.85008218
> view sel
> volume #2.2 level 0.03942
Unsupported scale factor (0.000000) detected on Display0
[Repeated 3 time(s)]
> open "/Users/tomforan/Library/CloudStorage/OneDrive-
> Birkbeck,UniversityofLondon/Temporary
> Maps/cryosparc_P501_J321_class_00_01200_volume.mrc"
> "/Users/tomforan/Library/CloudStorage/OneDrive-
> Birkbeck,UniversityofLondon/Temporary
> Maps/cryosparc_P501_J321_class_01_01200_volume.mrc"
Opened cryosparc_P501_J321_class_00_01200_volume.mrc as #4.1, grid size
128,128,128, pixel 1.66, shown at level 0.0828, step 1, values float32
Opened cryosparc_P501_J321_class_01_01200_volume.mrc as #4.2, grid size
128,128,128, pixel 1.66, shown at level 0.134, step 1, values float32
> open 6zpd
Summary of feedback from opening 6zpd fetched from pdb
---
notes | Fetching compressed mmCIF 6zpd from http://files.rcsb.org/download/6zpd.cif
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif
Fetching CCD TRS from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/TRS/TRS.cif
Fetching CCD VIV from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/VIV/VIV.cif
6zpd title:
gamma-tocopherol transfer protein [more info...]
Chain information for 6zpd #5
---
Chain | Description | UniProt
A | Alpha-tocopherol transfer protein | TTPA_HUMAN 48-278
Non-standard residues in 6zpd #5
---
CL — chloride ion
SO4 — sulfate ion
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
VIV —
(2R)-2,5,7,8-tetramethyl-2-[(4R,8R)-4,8,12-trimethyltridecyl]chroman-6-ol
6zpd mmCIF Assemblies
---
1| author_and_software_defined_assembly
29 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1904 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> open 6zph
Summary of feedback from opening 6zph fetched from pdb
---
notes | Fetching compressed mmCIF 6zph from http://files.rcsb.org/download/6zph.cif
Fetching CCD ADP from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ADP/ADP.cif
6zph title:
Kinesin binding protein complexed with Kif15 motor domain [more info...]
Chain information for 6zph #6
---
Chain | Description | UniProt
A | KIF-binding protein | KBP_HUMAN 1-621
B | Kinesin-like protein KIF15 | KIF15_HUMAN 1-374
Non-standard residues in 6zph #6
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
> fitmap #6 inMap #4.1
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_00_01200_volume.mrc
(#4.1) using 6226 atoms
average map value = 0.1135, steps = 180
shifted from previous position = 14.8
rotated from previous position = 35.3 degrees
atoms outside contour = 3766, contour level = 0.082781
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_00_01200_volume.mrc (#4.1) coordinates:
Matrix rotation and translation
0.81650764 -0.25769753 0.51663068 -0.45898497
0.26401238 0.96247091 0.06282681 -12.49460498
-0.51343231 0.08509833 0.85390019 55.66743832
Axis 0.01928500 0.89193574 0.45175074
Axis point 86.92248820 -0.00000000 32.28318332
Rotation angle (degrees) 35.27006673
Shift along axis 13.99457020
> volume #4.1 level 0.1626
> fitmap #6 inMap #4.1
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_00_01200_volume.mrc
(#4.1) using 6226 atoms
average map value = 0.1135, steps = 108
shifted from previous position = 0.00982
rotated from previous position = 0.0126 degrees
atoms outside contour = 4800, contour level = 0.16265
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_00_01200_volume.mrc (#4.1) coordinates:
Matrix rotation and translation
0.81638649 -0.25779981 0.51677109 -0.44211092
0.26414323 0.96243433 0.06283717 -12.50184082
-0.51355765 0.08520217 0.85381446 55.68126795
Axis 0.01936017 0.89190006 0.45181796
Axis point 86.92257846 0.00000000 32.26436466
Rotation angle (degrees) 35.28214350
Shift along axis 13.99884513
> fitmap #6 inMap #4.1
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_00_01200_volume.mrc
(#4.1) using 6226 atoms
average map value = 0.1135, steps = 76
shifted from previous position = 0.0174
rotated from previous position = 0.0265 degrees
atoms outside contour = 4800, contour level = 0.16265
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_00_01200_volume.mrc (#4.1) coordinates:
Matrix rotation and translation
0.81634997 -0.25808398 0.51668693 -0.41672214
0.26419724 0.96238997 0.06328789 -12.55346775
-0.51358791 0.08484220 0.85383210 55.71242869
Axis 0.01865696 0.89178442 0.45207573
Axis point 86.99475979 0.00000000 32.23267384
Rotation angle (degrees) 35.28527964
Shift along axis 13.98347512
> fitmap #6 inMap #4.2
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_01_01200_volume.mrc
(#4.2) using 6226 atoms
average map value = 0.1754, steps = 212
shifted from previous position = 24.2
rotated from previous position = 46 degrees
atoms outside contour = 3205, contour level = 0.13385
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_01_01200_volume.mrc (#4.2) coordinates:
Matrix rotation and translation
0.52825370 0.40631348 0.74555844 -43.89436843
-0.35253549 0.90376518 -0.24274931 69.43068757
-0.77244207 -0.13460259 0.62065722 139.15677629
Axis 0.06359511 0.89265226 -0.44623717
Axis point 114.19458209 0.00000000 130.88191857
Rotation angle (degrees) 58.24163592
Shift along axis -2.91093296
> volume #4.2 color #b2ffb29c
> volume #4.2 level 0.3379
> select add #6
75486 atoms, 76336 bonds, 43 pseudobonds, 5234 residues, 7 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.44128,-0.88245,0.16296,347.9,0.8934,0.41498,-0.17211,21.465,0.08425,0.22154,0.97151,162.32,#6,0.24423,0.66612,0.70473,-66.442,-0.36171,0.73686,-0.57114,159.37,-0.89973,-0.11542,0.4209,181.23
> view matrix models
> #1,0.054081,-0.99538,-0.07932,390.75,0.95717,0.074303,-0.27982,84.491,0.28442,-0.06079,0.95677,206.42,#6,0.60782,0.3675,0.70391,-31.68,-0.10465,0.9158,-0.38776,81.065,-0.78714,0.16202,0.59511,94.218
> view matrix models
> #1,-0.24114,-0.78358,0.57258,359.06,0.57837,-0.5898,-0.56357,237.19,0.77932,0.19526,0.59543,135.79,#6,0.070838,-0.060911,0.99563,-3.3073,0.5999,0.80005,0.0062637,-7.1798,-0.79693,0.59683,0.093215,130.55
> fitmap #6 inMap #4.2
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_01_01200_volume.mrc
(#4.2) using 6226 atoms
average map value = 0.1754, steps = 364
shifted from previous position = 36.3
rotated from previous position = 64.6 degrees
atoms outside contour = 5074, contour level = 0.3379
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_01_01200_volume.mrc (#4.2) coordinates:
Matrix rotation and translation
0.52837324 0.40635795 0.74544949 -43.89848246
-0.35250566 0.90376267 -0.24280194 69.43182850
-0.77237392 -0.13448512 0.62076749 139.12452985
Axis 0.06370042 0.89262198 -0.44628271
Axis point 114.18317344 0.00000000 130.88080350
Rotation angle (degrees) 58.23397757
Shift along axis -2.90884665
> view matrix models
> #1,-0.19425,-0.77314,0.60375,354.71,0.56155,-0.59229,-0.57779,238.84,0.80431,0.2268,0.54922,130.21,#6,0.48218,0.40108,0.77887,-47.963,-0.33651,0.90564,-0.25803,71.916,-0.80887,-0.13768,0.57164,152.92
> view sel
> select clear
> select add #6
6226 atoms, 6333 bonds, 15 pseudobonds, 774 residues, 4 models selected
> view sel
> view matrix models
> #6,-0.40631,0.39651,-0.82322,172.38,0.26245,0.91362,0.31052,-33.339,0.87523,-0.089885,-0.47528,80.832
> fitmap #6 inMap #4.2
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_01_01200_volume.mrc
(#4.2) using 6226 atoms
average map value = 0.1756, steps = 144
shifted from previous position = 12.2
rotated from previous position = 27.7 degrees
atoms outside contour = 5108, contour level = 0.3379
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_01_01200_volume.mrc (#4.2) coordinates:
Matrix rotation and translation
-0.71772120 0.44010120 -0.53961766 182.05107172
0.42507190 0.89071202 0.16107760 -35.75629507
0.55153437 -0.11376749 -0.82635755 149.92412401
Axis -0.24423406 -0.96962434 -0.01335541
Axis point 71.74011954 0.00000000 103.66739907
Rotation angle (degrees) 145.75953151
Shift along axis -11.79519631
> fitmap #4.1 inMap #4.2
Fit map cryosparc_P501_J321_class_00_01200_volume.mrc in map
cryosparc_P501_J321_class_01_01200_volume.mrc using 9665 points
correlation = 0.8435, correlation about mean = 0.3112, overlap = 924.1
steps = 156, shift = 2.46, angle = 44.3 degrees
Position of cryosparc_P501_J321_class_00_01200_volume.mrc (#4.1) relative to
cryosparc_P501_J321_class_01_01200_volume.mrc (#4.2) coordinates:
Matrix rotation and translation
0.76471150 -0.43264984 -0.47752533 121.65703621
0.56617173 0.80498612 0.17733282 -57.39908676
0.30767825 -0.40596979 0.86053624 22.76978220
Axis -0.41723789 -0.56165818 0.71445968
Axis point 168.21254292 187.53838610 0.00000000
Rotation angle (degrees) 44.34721729
Shift along axis -2.25316723
> fitmap #6 inMap #4.1
Fit molecule 6zph (#6) to map cryosparc_P501_J321_class_00_01200_volume.mrc
(#4.1) using 6226 atoms
average map value = 0.1274, steps = 340
shifted from previous position = 17.9
rotated from previous position = 54.8 degrees
atoms outside contour = 4432, contour level = 0.16265
Position of 6zph (#6) relative to
cryosparc_P501_J321_class_00_01200_volume.mrc (#4.1) coordinates:
Matrix rotation and translation
-0.47526998 0.84561550 -0.24300798 86.39833544
-0.24151031 0.14020285 0.96021661 17.36256056
0.84604446 0.51505106 0.13759066 -41.51085362
Axis -0.27790028 -0.67985489 -0.67865217
Axis point 56.85631841 0.00000000 1.62959264
Rotation angle (degrees) 126.77958382
Shift along axis -7.64271263
> volume #4.1 color #ffb2b2a3
Unsupported scale factor (0.000000) detected on Display0
[Repeated 1 time(s)]
> close #6
> close #2
> close #5
> show #!4.2 models
> close #4.2
> close #4.1
> cd
> /Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J327_map_sharp_all_classes_sharp/
Current working directory is:
/Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J327_map_sharp_all_classes_sharp
> open *.mrc vseries true
Opened map series J327_volume_class_00_map_sharp.mrc as #2, 10 images, grid
size 90,90,90, pixel 6.62, shown at level 1.87, step 1, values float32
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J327_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.9553, steps = 148
shifted from previous position = 36.7
rotated from previous position = 63.2 degrees
atoms outside contour = 64807, contour level = 1.8717
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J327_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.07961603 -0.74136797 0.66635941 308.00710149
0.99132877 0.12899178 0.02506863 81.95834690
-0.10453995 0.65858538 0.74520919 181.90298488
Axis 0.31684286 0.38555248 0.86657942
Axis point 136.88944302 122.93301850 0.00000000
Rotation angle (degrees) 91.32316327
Shift along axis 286.82247669
> select add #1
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.12946,-0.99051,0.046171,386.1,0.98845,0.12522,-0.085323,92.566,0.078732,0.056684,0.99528,207.42
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J327_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 1.164, steps = 56
shifted from previous position = 11.8
rotated from previous position = 5.95 degrees
atoms outside contour = 62446, contour level = 1.8717
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J327_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.10204025 -0.99471311 0.01156132 387.67674262
0.99472766 0.10214752 0.00910000 81.11397462
-0.01023284 0.01057180 0.99989178 209.99845036
Axis 0.00073976 0.01095426 0.99993973
Axis point 150.10938737 254.07160128 0.00000000
Rotation angle (degrees) 84.14335854
Shift along axis 211.16112598
> volume #2.1 level 0.4216
> close #2
> open "/Users/tomforan/Library/CloudStorage/OneDrive-
> Birkbeck,UniversityofLondon/Temporary
> Maps/cryosparc_P501_J245__localfilter.mrc"
Opened cryosparc_P501_J245__localfilter.mrc as #2, grid size 240,240,240,
pixel 0.828, shown at level 0.0988, step 1, values float32
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.10204,-0.99471,0.011561,194.43,0.99473,0.10215,0.0091,-11.521,-0.010233,0.010572,0.99989,32.687
> fitmap #1 inMap #2
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
cryosparc_P501_J245__localfilter.mrc (#2) using 69260 atoms
average map value = 0.02272, steps = 664
shifted from previous position = 46.9
rotated from previous position = 40.3 degrees
atoms outside contour = 65301, contour level = 0.098768
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
cryosparc_P501_J245__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.71740167 -0.69653141 -0.01337458 118.72587124
0.69372971 0.71601161 -0.07788791 -64.96193125
0.06382774 0.04659857 0.99687243 -16.01986152
Axis 0.08904888 -0.05522512 0.99449509
Axis point 140.34336266 113.73908254 0.00000000
Rotation angle (degrees) 44.34509434
Shift along axis -1.77173799
> view sel
> view matrix models
> #1,0.7174,-0.69653,-0.013375,119.64,0.69373,0.71601,-0.077888,-24.276,0.063828,0.046599,0.99687,-13.117
> fitmap #1 inMap #2
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
cryosparc_P501_J245__localfilter.mrc (#2) using 69260 atoms
average map value = 0.05265, steps = 448
shifted from previous position = 20.7
rotated from previous position = 44.3 degrees
atoms outside contour = 58430, contour level = 0.098768
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
cryosparc_P501_J245__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.99999758 -0.00170744 0.00140206 0.05580501
0.00170665 0.99999840 0.00057704 -0.19947271
-0.00140304 -0.00057464 0.99999887 0.12139369
Axis -0.25221399 0.61430684 0.74767319
Axis point 100.40124062 25.76715776 0.00000000
Rotation angle (degrees) 0.13081459
Shift along axis -0.04584945
> fitmap #1 inMap #2
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
cryosparc_P501_J245__localfilter.mrc (#2) using 69260 atoms
average map value = 0.05265, steps = 44
shifted from previous position = 0.00204
rotated from previous position = 0.00152 degrees
atoms outside contour = 58433, contour level = 0.098768
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
cryosparc_P501_J245__localfilter.mrc (#2) coordinates:
Matrix rotation and translation
0.99999762 -0.00170538 0.00137751 0.05628982
0.00170458 0.99999840 0.00058671 -0.19933639
-0.00137850 -0.00058436 0.99999890 0.11917325
Axis -0.25805113 0.60729831 0.75139761
Axis point 100.56525584 25.89952372 0.00000000
Rotation angle (degrees) 0.13000859
Shift along axis -0.04603581
> view sel
> volume #2 color #99bfe596
> select clear
> volume #2 level 0.05451
> volume #2 level 0.04197
> lighting simple
> close #2
> cd
> /Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J306_map_sharp_all_classes_sharp/
Current working directory is:
/Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J306_map_sharp_all_classes_sharp
> open *.mrc vseries true
Opened map series J306_volume_class_00_map_sharp.mrc as #2, 6 images, grid
size 90,90,90, pixel 3.31, shown at level 1.09, step 1, values float32
> select add #1
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 3 models selected
> view matrix models
> #1,1,-0.0017054,0.0013775,32.47,0.0017046,1,0.00058671,33.539,-0.0013785,-0.00058436,1,-1.5586
> fitmap #1 inMap #3
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
2DC+linker_2Kif_P501_J290.mrc (#3) using 69260 atoms
average map value = 0.06753, steps = 396
shifted from previous position = 61.8
rotated from previous position = 50.3 degrees
atoms outside contour = 49739, contour level = 0.048308
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
2DC+linker_2Kif_P501_J290.mrc (#3) coordinates:
Matrix rotation and translation
0.88705537 0.41392843 0.20444088 -36.38172945
-0.44329956 0.64004555 0.62755655 66.42663515
0.12891202 -0.64730595 0.75125012 134.57732436
Axis -0.82884363 0.04910460 -0.55732125
Axis point 0.00000000 175.37058929 -8.51442482
Rotation angle (degrees) 50.26963376
Shift along axis -41.58618411
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J306_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.2042, steps = 112
shifted from previous position = 33.1
rotated from previous position = 8.99 degrees
atoms outside contour = 64890, contour level = 1.0878
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J306_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.85473341 0.38970244 0.34287441 -12.70609069
-0.51561910 0.56143623 0.64724520 68.11214428
0.05973092 -0.73001467 0.68081630 153.43700592
Axis -0.82356713 0.16931276 -0.54135975
Axis point 0.00000000 168.09356882 -7.31097396
Rotation angle (degrees) 56.73631543
Shift along axis -61.06804502
> view matrix models
> #1,0.85473,0.3897,0.34287,13.584,-0.51562,0.56144,0.64725,84.745,0.059731,-0.73001,0.68082,152.72
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J306_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.2462, steps = 140
shifted from previous position = 21.9
rotated from previous position = 19.1 degrees
atoms outside contour = 64042, contour level = 1.0878
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J306_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.65356477 0.53668896 0.53368352 0.47084291
-0.74464110 0.32970406 0.58034894 157.21699546
0.13550924 -0.77669830 0.61512360 161.02961551
Axis -0.71109785 0.20864482 -0.67142177
Axis point 0.00000000 184.21403900 -85.33363161
Rotation angle (degrees) 72.59066804
Shift along axis -75.65109321
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J306_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.2462, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.0222 degrees
atoms outside contour = 64031, contour level = 1.0878
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J306_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.65370894 0.53643753 0.53375974 0.48119741
-0.74451235 0.32959131 0.58057812 157.20533375
0.13552131 -0.77691981 0.61484113 161.08277509
Axis -0.71130468 0.20866983 -0.67119487
Axis point 0.00000000 184.22850046 -85.23248134
Rotation angle (degrees) 72.59820526
Shift along axis -75.65620022
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.72624,0.68535,-0.053539,31.92,-0.68741,0.72335,-0.065011,169.46,-0.0058272,0.084017,0.99645,47.826
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J306_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4826, steps = 68
shifted from previous position = 7.55
rotated from previous position = 12.1 degrees
atoms outside contour = 58630, contour level = 1.0878
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J306_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.58021614 0.81446255 -0.00019100 25.36089842
-0.81446255 0.58021607 -0.00031870 191.37489425
-0.00014874 0.00034048 0.99999995 62.90679731
Axis 0.00040467 -0.00002594 -0.99999992
Axis point 198.34389269 71.05939500 0.00000000
Rotation angle (degrees) 54.53425934
Shift along axis -62.90149451
> volume #2.1 level 0.5999
> volume #2.1 color #d1d3d5
> volume #2.1 color #d1d3d590
> select clear
> volume #2.1 level 0.2857
> volume #2.2 level 0.1505
> volume #2.4 level 0.05759
> volume #2.4 level 0.6151
> volume #2.4 level 0.2434
> volume #2.4 level 0.6538
> volume #2.4 level 0.3828
> volume #2.3 level 0.25
Unsupported scale factor (0.000000) detected on Display0
[Repeated 5 time(s)]
> close #2
> cd
> /Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J341_map_sharp_all_classes_sharp/
Current working directory is:
/Users/tomforan/Desktop/temporary_maps_desktop/cryosparc_P501_J341_map_sharp_all_classes_sharp
> open *.mrc vseries true
Opened map series J341_volume_class_00_map_sharp.mrc as #2, 6 images, grid
size 90,90,90, pixel 3.31, shown at level 1.02, step 1, values float32
> volume #2.1 level 0.4555
> select add #1
69260 atoms, 70003 bonds, 28 pseudobonds, 4460 residues, 3 models selected
> view matrix models
> #1,0.59035,0.80715,0.00017213,25.261,-0.80714,0.59034,-0.00489,190.12,-0.0040486,0.0027479,0.99999,62.977
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.59035,0.80715,0.00017213,27.576,-0.80714,0.59034,-0.00489,183.27,-0.0040486,0.0027479,0.99999,15.322
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J341_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.4061, steps = 72
shifted from previous position = 9.76
rotated from previous position = 0.679 degrees
atoms outside contour = 41180, contour level = 0.45548
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J341_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.58169274 0.81340848 -0.00050918 25.43390972
-0.81340850 0.58169288 0.00019860 190.75964953
0.00045773 0.00029864 0.99999987 22.06891975
Axis 0.00006150 -0.00059436 -0.99999982
Axis point 198.17322565 70.64350939 0.00000000
Rotation angle (degrees) 54.43031173
Shift along axis -22.18073071
> view matrix models
> #1,0.58169,0.81341,-0.00050918,1.9879,-0.81341,0.58169,0.0001986,140.19,0.00045773,0.00029864,1,14.402
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J341_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.3869, steps = 116
shifted from previous position = 11.6
rotated from previous position = 26.9 degrees
atoms outside contour = 42335, contour level = 0.45548
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J341_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.88671728 0.46231150 -0.00077223 1.30637812
-0.46231114 0.88671760 0.00058820 83.10553465
0.00095669 -0.00016455 0.99999955 12.61810718
Axis -0.00081412 -0.00186986 -0.99999792
Axis point 170.17837953 38.89649216 0.00000000
Rotation angle (degrees) 27.53641478
Shift along axis -12.77454005
> view matrix models
> #1,0.88672,0.46231,-0.00077223,6.8393,-0.46231,0.88672,0.0005882,83.545,0.00095669,-0.00016455,1,79.641
> fitmap #1 inMap #2.1
Fit molecule 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) to map
J341_volume_class_00_map_sharp.mrc (#2.1) using 69260 atoms
average map value = 0.3967, steps = 68
shifted from previous position = 15.5
rotated from previous position = 0.0617 degrees
atoms outside contour = 41304, contour level = 0.45548
Position of 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb (#1) relative to
J341_volume_class_00_map_sharp.mrc (#2.1) coordinates:
Matrix rotation and translation
0.88632938 0.46305324 -0.00140425 1.39488700
-0.46305249 0.88633049 0.00083416 83.23425991
0.00163090 -0.00008910 0.99999868 94.04555879
Axis -0.00099692 -0.00327731 -0.99999413
Axis point 169.55583224 38.81338141 0.00000000
Rotation angle (degrees) 27.58445405
Shift along axis -94.31918182
> volume #2.1 level 0.3598
> select clear
> volume #2.1 level 0.22
> volume #2.3 level 0.169
> select /B:43
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
63 atoms, 62 bonds, 4 residues, 1 model selected
> select up
5575 atoms, 5617 bonds, 358 residues, 1 model selected
> molmap sel 12 onGrid #2.1
Opened 2DCLK_2Kif3A_fitted_P501_J219_modelled.pdb map 12 as #5, grid size
90,90,90, pixel 3.31, shown at level 0.0518, step 1, values float32
No map chosen to save
> save /Users/tomforan/Library/CloudStorage/OneDrive-
> Birkbeck,UniversityofLondon/references/KifMD_P501J341.mrc models #5
Unsupported scale factor (0.000000) detected on Display0
[Repeated 3 time(s)]An error occurred in drawing the scene. Redrawing graphics
is now stopped to avoid a continuous stream of error messages. To restart
graphics use the command "graphics restart" after changing the settings that
caused the error.
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glBlitFramebuffer,
cArguments = (
0,
0,
2348,
1740,
0,
0,
2348,
1740,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
Traceback (most recent call last):
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/updateloop.py", line 84, in draw_new_frame
view.draw(check_for_changes = False)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 278, in _draw_scene
offscreen.finish(r)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1867, in finish
cfb.copy_from_framebuffer(fb, depth=False)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2414, in copy_from_framebuffer
GL.glBlitFramebuffer(0, 0, w, h, 0, 0, w, h, what, GL.GL_NEAREST)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glBlitFramebuffer,
cArguments = (
0,
0,
2348,
1740,
0,
0,
2348,
1740,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
Traceback (most recent call last):
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py", line 115, in _redraw
self.render()
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/sideview/tool.py", line 310, in render
self.view.draw()
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 188, in draw
self._draw_scene(camera, drawings)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/view.py", line 278, in _draw_scene
offscreen.finish(r)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1867, in finish
cfb.copy_from_framebuffer(fb, depth=False)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 2414, in copy_from_framebuffer
GL.glBlitFramebuffer(0, 0, w, h, 0, 0, w, h, what, GL.GL_NEAREST)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glBlitFramebuffer,
cArguments = (
0,
0,
1490,
52,
0,
0,
1490,
52,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
Error processing trigger "frame drawn":
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glBlitFramebuffer,
cArguments = (
0,
0,
1490,
52,
0,
0,
1490,
52,
GL_COLOR_BUFFER_BIT,
GL_NEAREST,
)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Traceback (most recent call last):
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 98, in _expose_event
self.status(self._last_message, self._last_color)
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/statusbar.py", line 164, in status
r.draw_background()
File
"/private/var/folders/2r/qhkfdw750gx2px47fpk_w2br0000gn/T/AppTranslocation/7F62CD4E-C1D2-4027-A589-47AEF404F26A/d/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/opengl.py", line 1238, in draw_background
GL.glClear(flags)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
OpenGL.error.GLError: GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
File "src/errorchecker.pyx", line 59, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
See log for complete Python traceback.
Unsupported scale factor (0.000000) detected on Display0
[Repeated 5 time(s)]
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK193B/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 Performance and 2 Efficiency)
Memory: 16 GB
System Firmware Version: 18000.120.36
OS Loader Version: 18000.120.36
Software:
System Software Overview:
System Version: macOS 26.5 (25F71)
Kernel Version: Darwin 25.5.0
Time since boot: 11 days, 7 hours, 52 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.12.1
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.1
attrs: 25.4.0
babel: 2.17.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.12.2
build: 1.3.0
certifi: 2025.7.14
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.26.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ISOLDE: 1.11.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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