Opened 3 weeks ago

Last modified 3 weeks ago

#20424 assigned defect

glBlitFramebuffer: invalid framebuffer operation after Unsupported scale factor detected

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
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:        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

Change History (2)

comment:1 by Eric Pettersen, 3 weeks ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → glBlitFramebuffer: invalid framebuffer operation after Unsupported scale factor detected

comment:2 by Tom Goddard, 3 weeks ago

Report shows only Mac laptop display was in use. But I suspect ChimeraX was started on an external display, then the display was disconnected, and somehow Qt didn't handle the display disconnect correctly, hence the scale factor 0 warnings that we have seen many times before.

It may be that our OpenGL context is still associated with the disconnected display. This reports shows tracebacks for both our main graphics rendering and statusline rendering. Our OpenGL context code keeps a reference to th QScreen the context was created on. Should check if that code has problems. Should also try starting ChimeraX on external display then unplugging that display.

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