wrapped C/C++ object of type QScreen has been deleted

[paulino@…]

The following bug report has been submitted:
Platform:        macOS-10.15.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
tried to open .mrc map downloaded from cryosparc and got the error described

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/joanapaulino/Downloads/cryosparc_P64_J565_map.mrc format mrc

Opened cryosparc_P64_J565_map.mrc as #1, grid size 320,320,320, pixel 1.33,
shown at level 0.306, step 2, values float32  

> volume #1 level 0.4745

> volume #1 level 0.4698

> close #1

> open /Users/joanapaulino/Downloads/cryosparc_P64_J567_map.mrc format mrc

Opened cryosparc_P64_J567_map.mrc as #1, grid size 320,320,320, pixel 1.33,
shown at level 0.302, step 2, values float32  

> volume #1 level 0.4068

> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/Nef.pdb" format pdb

Chain information for Nef.pdb #2  
---  
Chain | Description  
N | No description available  
  

> select #2

1047 atoms, 1081 bonds, 1 pseudobond, 133 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #2,1,0,0,-3.1026,0,1,0,103.26,0,0,1,75.197

> view matrix models #2,1,0,0,24.587,0,1,0,77.14,0,0,1,109.33

> view matrix models #2,1,0,0,22.293,0,1,0,79.712,0,0,1,110.85

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.93307,-0.35405,0.063472,72.575,0.18142,0.31085,-0.93298,245.28,0.3106,0.88205,0.35428,16.822

> ui tool show "Fit in Map"

Fit molecule Nef.pdb (#2) to map cryosparc_P64_J567_map.mrc (#1) using 1047
atoms  
average map value = 0.4278, steps = 216  
shifted from previous position = 35.4  
rotated from previous position = 48.8 degrees  
atoms outside contour = 339, contour level = 0.40677  
  
Position of Nef.pdb (#2) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.87433761 -0.44569008 -0.19207835 146.74048628  
0.34929937 0.85267497 -0.38850398 90.36995714  
0.33693277 0.27259079 0.90120506 61.51035367  
Axis 0.56921020 -0.45548465 0.68449506  
Axis point -246.21699054 290.78701746 -0.00000000  
Rotation angle (degrees) 35.50066062  
Shift along axis 84.46758583  
  

> view matrix models
> #2,-0.57024,0.49588,-0.65493,268.25,0.68964,0.72216,-0.053672,25.766,0.44635,-0.48227,-0.75378,321.6

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.57024,0.49588,-0.65493,264.04,0.68964,0.72216,-0.053672,29.732,0.44635,-0.48227,-0.75378,294.9

> volume #1 level 0.4889

> view matrix models
> #2,-0.57024,0.49588,-0.65493,260.3,0.68964,0.72216,-0.053672,21.754,0.44635,-0.48227,-0.75378,291.99

> view matrix models
> #2,-0.57024,0.49588,-0.65493,249.12,0.68964,0.72216,-0.053672,30.88,0.44635,-0.48227,-0.75378,298.73

Fit molecule Nef.pdb (#2) to map cryosparc_P64_J567_map.mrc (#1) using 1047
atoms  
average map value = 0.4078, steps = 116  
shifted from previous position = 15.8  
rotated from previous position = 21.6 degrees  
atoms outside contour = 916, contour level = 0.48891  
  
Position of Nef.pdb (#2) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.80417606 0.36002470 -0.47295144 288.31046373  
0.55080217 0.75046024 -0.36527577 68.80885664  
0.22342295 -0.55424871 -0.80180455 353.89929024  
Axis -0.25319483 -0.93303513 0.25561262  
Axis point 96.86720360 0.00000000 215.05586764  
Rotation angle (degrees) 158.08831871  
Shift along axis -46.73867394  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.49016,-0.49013,0.72078,98.619,-0.11841,-0.8567,-0.50203,392.15,0.86355,0.16073,-0.47796,135.12

Opened Nef.pdb map 5 as #3, grid size 46,37,45, pixel 1.67, shown at level
0.0848, step 1, values float32  
Fit map Nef.pdb map 5 in map cryosparc_P64_J567_map.mrc using 4186 points  
correlation = 0.8546, correlation about mean = 0.1208, overlap = 567.7  
steps = 180, shift = 5.53, angle = 49.1 degrees  
  
Position of Nef.pdb map 5 (#3) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.19603024 -0.23578218 0.95182924 134.11342861  
0.26326783 -0.94768006 -0.18053408 319.75337294  
0.94459631 0.21519588 0.24784781 35.17876644  
Axis 0.62128880 0.01135557 0.78349938  
Axis point 19.88289311 166.19130797 0.00000000  
Rotation angle (degrees) 161.42927284  
Shift along axis 114.51669370  
  
Average map value = 0.4042 for 1047 atoms, 891 outside contour  

> show #!3 models

> select #3

2 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.19603,-0.23578,0.95183,85.784,0.26327,-0.94768,-0.18053,295.15,0.9446,0.2152,0.24785,40.671

> volume #1 level 0.4022

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.2611,0.035366,0.96466,-15.044,0.56521,-0.81572,-0.12308,229.62,0.78254,0.57737,-0.23297,66.015

> view matrix models
> #3,0.19313,-0.022427,0.98092,0.34507,0.51754,-0.84702,-0.12126,240.21,0.83358,0.53109,-0.15198,56.495

> view matrix models
> #3,0.1536,-0.052543,0.98674,9.2159,0.49037,-0.86289,-0.12228,246.19,0.85787,0.50265,-0.10677,52.109

> view matrix models
> #3,0.21232,-0.30801,0.92739,41.378,-0.35504,-0.90849,-0.22045,379.9,0.91042,-0.28246,-0.30225,170.08

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.21232,-0.30801,0.92739,38.848,-0.35504,-0.90849,-0.22045,403.12,0.91042,-0.28246,-0.30225,162.53

> view matrix models
> #3,0.21232,-0.30801,0.92739,76.95,-0.35504,-0.90849,-0.22045,417.79,0.91042,-0.28246,-0.30225,159.71

> view matrix models
> #3,0.21232,-0.30801,0.92739,75.405,-0.35504,-0.90849,-0.22045,408.38,0.91042,-0.28246,-0.30225,155.59

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.055116,0.30423,0.951,13.211,-0.29955,-0.90354,0.3064,344.06,0.95249,-0.30176,0.041331,115.82

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.055116,0.30423,0.951,13.928,-0.29955,-0.90354,0.3064,348.43,0.95249,-0.30176,0.041331,118.57

> view matrix models
> #3,0.055116,0.30423,0.951,14.881,-0.29955,-0.90354,0.3064,344.79,0.95249,-0.30176,0.041331,118.08

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.42549,0.5685,-0.7041,222.16,0.89764,0.16639,-0.40811,112.31,-0.11486,-0.80568,-0.58111,399.25

Opened Nef.pdb map 10 as #3, grid size 32,28,32, pixel 3.33, shown at level
0.044, step 1, values float32  
Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 834 points  
correlation = 0.8999, correlation about mean = 0.368, overlap = 69.89  
steps = 52, shift = 0.932, angle = 2.55 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.20408606 -0.24557672 0.94765022 137.41751491  
0.30459029 -0.93590504 -0.17693644 312.47875440  
0.93036209 0.25253480 0.26580545 30.91300169  
Axis 0.61514681 0.02476240 0.78802362  
Axis point 21.24389626 163.26286518 0.00000000  
Rotation angle (degrees) 159.56892891  
Shift along axis 116.62984521  
  
Average map value = 0.4028 for 1047 atoms, 472 outside contour  
Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 834 points  
correlation = 0.8999, correlation about mean = 0.3672, overlap = 69.89  
steps = 40, shift = 0.0233, angle = 0.0446 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.20379792 -0.24492655 0.94788047 137.26173828  
0.30467812 -0.93598777 -0.17634660 312.43700860  
0.93039650 0.25285937 0.26537612 30.90026117  
Axis 0.61529689 0.02506450 0.78789689  
Axis point 21.20175468 163.21040328 0.00000000  
Rotation angle (degrees) 159.58731375  
Shift along axis 116.63401787  
  
Average map value = 0.4027 for 1047 atoms, 472 outside contour  

> show #!3 models

> select #3.1

1 model selected  

> select #3

2 models selected  

> view matrix models
> #3,0.29672,-0.34104,0.89199,86.484,0.94531,0.23738,-0.2237,71.953,-0.13545,0.90959,0.39282,77.836

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.29672,-0.34104,0.89199,124.91,0.94531,0.23738,-0.2237,197.23,-0.13545,0.90959,0.39282,91.972

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.71554,-0.22913,-0.65992,216.79,-0.45618,0.56217,-0.68982,398.18,0.52905,0.79465,0.29773,25.091

> view matrix models
> #3,0.79282,0.043306,0.60792,34.918,0.56887,-0.41052,-0.71265,387.93,0.2187,0.91082,-0.3501,121.59

> volume #3 level 0.3071

> view matrix models
> #3,0.097984,-0.28112,0.95466,138.08,0.926,-0.32567,-0.19094,271.74,0.36458,0.90272,0.22841,41.152

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.097984,-0.28112,0.95466,91.141,0.926,-0.32567,-0.19094,147.73,0.36458,0.90272,0.22841,18.708

Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 198 points  
correlation = 0.9781, correlation about mean = 0.031, overlap = 30.73  
steps = 68, shift = 2.78, angle = 8.25 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.19333828 -0.18586406 0.96336642 124.12678606  
0.16990158 -0.97340075 -0.15370241 332.39489422  
0.96630935 0.13396092 0.21977423 45.51117444  
Axis 0.62873957 -0.00643230 0.77758934  
Axis point 18.83480888 170.42196652 0.00000000  
Rotation angle (degrees) 166.77580912  
Shift along axis 111.29436167  
  
Average map value = 0.4003 for 1047 atoms, 474 outside contour  

> view matrix models
> #3,-0.19334,-0.18586,0.96337,91.571,0.1699,-0.9734,-0.1537,384.47,0.96631,0.13396,0.21977,47.321

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.7151,0.3776,0.58826,-70.304,0.63584,-0.0017394,-0.77182,254.85,-0.29041,0.92597,-0.24133,163.99

> view matrix models
> #3,0.46178,0.20176,0.86375,-40.759,0.88698,-0.098376,-0.45122,199.04,-0.0060652,0.97448,-0.22438,116.26

> view matrix models
> #3,0.93978,-0.31228,0.1389,38.849,0.088507,0.61489,0.78363,83.051,-0.33012,-0.72415,0.6055,301.44

> view matrix models
> #3,0.28718,0.61974,0.73038,-58.575,-0.94143,0.041911,0.3346,350.38,0.17676,-0.78369,0.59547,240.23

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.28718,0.61974,0.73038,-52.094,-0.94143,0.041911,0.3346,299.95,0.17676,-0.78369,0.59547,229.69

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.4222,0.88086,0.2141,-51.179,-0.80046,0.25142,0.54411,230.07,0.42545,-0.4011,0.81124,120.96

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.4222,0.88086,0.2141,-48.31,-0.80046,0.25142,0.54411,233.44,0.42545,-0.4011,0.81124,126.49

Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 198 points  
correlation = 0.9781, correlation about mean = 0.03124, overlap = 30.73  
steps = 60, shift = 0.0225, angle = 0.125 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.19441784 -0.18625022 0.96307453 124.35131550  
0.17172700 -0.97310856 -0.15352383 332.09840778  
0.96576992 0.13553813 0.22117385 45.24266068  
Axis 0.62822967 -0.00585799 0.77800589  
Axis point 18.97574678 170.29447584 0.00000000  
Rotation angle (degrees) 166.69935245  
Shift along axis 111.37481370  
  
Average map value = 0.4004 for 1047 atoms, 475 outside contour  

> view matrix models
> #3,-0.19442,-0.18625,0.96307,54.115,0.17173,-0.97311,-0.15352,370.41,0.96577,0.13554,0.22117,41.273

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.066815,-0.40302,0.91275,52.357,-0.89387,0.38227,0.23422,294.95,-0.44331,-0.83153,-0.33471,425.43

> ~select #3

Nothing selected  

> open "/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2
> structures/Ap2_deltacomp.pdb" format pdb

Chain information for Ap2_deltacomp.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
M | No description available  
S | No description available  
  

> select #4

10528 atoms, 10715 bonds, 1432 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-2.251,0,1,0,30.007,0,0,1,105.93

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.72707,0.65895,0.19277,-83.672,0.66728,-0.61214,-0.42428,222.26,-0.16158,0.43711,-0.88477,347.09

> view matrix models
> #4,0.71834,0.43279,0.54468,-101.82,0.53166,-0.84647,-0.028595,218.44,0.44868,0.31013,-0.83816,264.08

> volume #1 zflip

Expected a keyword  

> volume #1 flipNormals

Missing "flipNormals" keyword's argument  

> volume zflip #1

Expected a density maps specifier or a keyword  

> volume flip #1

Opened cryosparc_P64_J567_map.mrc z flip as #5, grid size 320,320,320, pixel
1.33, shown at step 1, values float32  

> select #1

2 models selected  

> view matrix models
> #1,0.94909,-0.30564,-0.076181,89.85,0.24296,0.86425,-0.4405,67.543,0.20047,0.39957,0.89451,-103.53

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.76541,-0.41752,-0.48971,237.07,-0.4846,0.12677,-0.8655,461.85,0.42344,0.89978,-0.1053,-48.454

> view matrix models
> #1,0.60585,-0.36375,-0.70755,304.52,-0.68324,0.21773,-0.69697,450.26,0.40758,0.90569,-0.11662,-43.994

> select #5

2 models selected  

> view matrix models
> #5,0.4477,0.89066,-0.079315,-50.979,0.76536,-0.42756,-0.48106,239.54,-0.46237,0.15467,-0.87309,473.64

> select #4

10528 atoms, 10715 bonds, 1432 residues, 1 model selected  

> view matrix models
> #4,0.043991,0.99877,-0.022833,4.9317,0.98309,-0.047344,-0.17689,55.233,-0.17775,-0.014666,-0.98397,429.49

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.043991,0.99877,-0.022833,45.775,0.98309,-0.047344,-0.17689,43.719,-0.17775,-0.014666,-0.98397,358.47

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.87758,0.46162,-0.12949,10.104,0.44033,-0.88288,-0.16317,246.25,-0.18965,0.086178,-0.97806,344.89

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.87758,0.46162,-0.12949,8.5949,0.44033,-0.88288,-0.16317,266.39,-0.18965,0.086178,-0.97806,353.98

> view matrix models
> #4,0.87758,0.46162,-0.12949,28.216,0.44033,-0.88288,-0.16317,266.62,-0.18965,0.086178,-0.97806,349.03

Fit molecule Ap2_deltacomp.pdb (#4) to map cryosparc_P64_J567_map.mrc z flip
(#5) using 10528 atoms  
average map value = 0.504, steps = 152  
shifted from previous position = 15.9  
rotated from previous position = 10.6 degrees  
atoms outside contour = 2692, contour level = 0.40221  
  
Position of Ap2_deltacomp.pdb (#4) relative to cryosparc_P64_J567_map.mrc z
flip (#5) coordinates:  
Matrix rotation and translation  
0.85886822 -0.36085971 0.36349092 85.14213916  
0.46895092 0.83941481 -0.27471405 68.38652369  
-0.20598643 0.40640257 0.89017220 96.75963346  
Axis 0.56047877 0.46861279 0.68283643  
Axis point 2.76337619 8.34934762 0.00000000  
Rotation angle (degrees) 37.41763745  
Shift along axis 145.83816461  
  

> view matrix models
> #4,0.81853,0.55384,-0.15254,40.643,0.55593,-0.83059,-0.032566,228.71,-0.14474,-0.058147,-0.98776,360.19

> select #3

2 models selected  

> view matrix models
> #3,0.066815,-0.40302,0.91275,66.179,-0.89387,0.38227,0.23422,298.86,-0.44331,-0.83153,-0.33471,443.42

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.16534,-0.5302,0.83159,124.05,-0.8394,0.51832,0.16358,280.52,-0.51776,-0.67099,-0.53075,452.95

> view matrix models
> #3,0.59472,0.30448,0.74404,-84.169,-0.78725,0.033017,0.61575,290.57,0.16292,-0.95195,0.25934,312.61

> view matrix models
> #3,-0.71534,-0.35494,-0.60191,328.65,0.6534,-0.64509,-0.39613,289.19,-0.24768,-0.67666,0.69339,286.55

> view matrix models
> #3,0.955,-0.28515,-0.081657,32.6,0.031432,-0.17646,0.98381,166.22,-0.29494,-0.9421,-0.15956,419.15

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.955,-0.28515,-0.081657,122.6,0.031432,-0.17646,0.98381,118.03,-0.29494,-0.9421,-0.15956,406.47

> view matrix models
> #3,0.955,-0.28515,-0.081657,89.505,0.031432,-0.17646,0.98381,98.311,-0.29494,-0.9421,-0.15956,420.3

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.14796,-0.88965,-0.432,360.73,0.66349,-0.41322,0.62372,80.657,-0.73341,-0.19434,0.65142,294.69

Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 198
points  
correlation = 0.9648, correlation about mean = 0.05386, overlap = 30.18  
steps = 244, shift = 23.4, angle = 62.1 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
0.91197230 0.37145202 0.17415484 -23.69769214  
0.40935666 -0.85194738 -0.32651612 303.18567925  
0.02708569 0.36906510 -0.92900877 250.83238238  
Axis 0.97698296 0.20656690 0.05323920  
Axis point 0.00000000 130.74021255 153.58738027  
Rotation angle (degrees) 159.14621711  
Shift along axis 52.82999988  
  

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.77074,-0.62176,-0.13916,156.22,0.50993,0.47101,0.7198,-69.407,-0.382,-0.62574,0.68009,336.83

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.59228,-0.80278,0.068866,183.23,0.31618,0.31018,0.89656,-39.673,-0.7411,-0.50924,0.43754,396.66

> volume #3 level 0.2017

> view matrix models
> #3,0.18126,-0.95508,0.23447,243.11,0.25529,0.27594,0.92665,-29.827,-0.94972,-0.1081,0.29384,387.07

> view matrix models
> #3,0.18681,-0.93244,0.30929,231.37,-0.11658,0.29157,0.94942,17.255,-0.97545,-0.21342,-0.054237,441.67

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.18681,-0.93244,0.30929,268.22,-0.11658,0.29157,0.94942,23.97,-0.97545,-0.21342,-0.054237,408.93

> view matrix models
> #3,0.18681,-0.93244,0.30929,261.32,-0.11658,0.29157,0.94942,46.929,-0.97545,-0.21342,-0.054237,416.74

> ui mousemode right "rotate selected models"

> view matrix models
> #3,0.55506,-0.60571,-0.57012,259.69,0.61514,-0.16247,0.7715,25.144,-0.55993,-0.77892,0.28242,399.2

> ui mousemode right "translate selected models"

> view matrix models
> #3,0.55506,-0.60571,-0.57012,258.49,0.61514,-0.16247,0.7715,28.259,-0.55993,-0.77892,0.28242,399.66

> view matrix models
> #3,0.55506,-0.60571,-0.57012,257.73,0.61514,-0.16247,0.7715,28.259,-0.55993,-0.77892,0.28242,400.26

Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422
points  
correlation = 0.9244, correlation about mean = 0.1079, overlap = 52.42  
steps = 100, shift = 1.78, angle = 28 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
0.91427140 0.09203474 0.39450906 -16.52334862  
0.26902592 -0.86603913 -0.42142765 336.22461469  
0.30287430 0.49143242 -0.81655454 187.83271143  
Axis 0.97698536 0.09807179 0.18942421  
Axis point 0.00000000 146.36611613 137.53169526  
Rotation angle (degrees) 152.14846685  
Shift along axis 52.41114204  
  

> hide #!3 models

> select #2

1047 atoms, 1081 bonds, 1 pseudobond, 133 residues, 2 models selected  

> view matrix models
> #2,-0.19442,-0.18625,0.96307,122.87,0.17173,-0.97311,-0.15352,340.19,0.96577,0.13554,0.22117,62.638

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.44461,0.89542,-0.023355,-7.7266,0.55046,-0.25257,0.79574,91.223,0.70662,-0.36665,-0.60519,252.77

> view matrix models
> #2,0.48612,0.86829,-0.098813,-1.8995,0.75099,-0.35725,0.55533,102.8,0.44689,-0.34416,-0.82574,308.79

> view matrix models
> #2,0.50968,0.85745,-0.070766,-6.6396,0.76575,-0.4146,0.49166,115.16,0.39223,-0.30478,-0.86791,315.47

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.50968,0.85745,-0.070766,23.456,0.76575,-0.4146,0.49166,104.24,0.39223,-0.30478,-0.86791,309.21

> view matrix models
> #2,0.50968,0.85745,-0.070766,0.34037,0.76575,-0.4146,0.49166,74.535,0.39223,-0.30478,-0.86791,323.14

Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422
points  
correlation = 0.9243, correlation about mean = 0.1078, overlap = 52.42  
steps = 44, shift = 0.0165, angle = 0.019 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
0.91430258 0.09215302 0.39440917 -16.53749166  
0.26916167 -0.86589103 -0.42164522 336.22291980  
0.30265948 0.49167115 -0.81649047 187.81632315  
Axis 0.97699233 0.09814643 0.18934961  
Axis point 0.00000000 146.35562024 137.54670997  
Rotation angle (degrees) 152.13354858  
Shift along axis 52.40502232  
  
Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422
points  
correlation = 0.9243, correlation about mean = 0.1078, overlap = 52.42  
steps = 40, shift = 0.023, angle = 0.0235 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
0.91429158 0.09182094 0.39451211 -16.49750921  
0.26887499 -0.86602061 -0.42156201 336.25180272  
0.30294740 0.49150504 -0.81648371 187.80987684  
Axis 0.97699016 0.09797508 0.18944947  
Axis point 0.00000000 146.37500340 137.53246006  
Rotation angle (degrees) 152.14175105  
Shift along axis 52.40687549  
  
Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422
points  
correlation = 0.9491, correlation about mean = 0.2295, overlap = 53.81  
steps = 248, shift = 14.9, angle = 76.3 degrees  
  
Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip
(#5) coordinates:  
Matrix rotation and translation  
-0.04595522 0.08887634 0.99498196 55.61281617  
-0.73146668 0.67535164 -0.09410974 230.24948794  
-0.68032684 -0.73212099 0.03397415 400.00854804  
Axis -0.32362265 0.84977792 -0.41610800  
Axis point 272.54567402 0.00000000 226.96673308  
Rotation angle (degrees) 99.68984739  
Shift along axis 11.21660864  
  
Average map value = 0.3896 for 1047 atoms, 491 outside contour  

> ~select #2

Nothing selected  

> open /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/dmSer_monomer.pdb
> format pdb

Chain information for dmSer_monomer.pdb #6  
---  
Chain | Description  
B | No description available  
  

> select #6

2967 atoms, 3040 bonds, 3 pseudobonds, 367 residues, 2 models selected  

> view matrix models #6,1,0,0,-104.98,0,1,0,-15.13,0,0,1,92.406

> set bgColor white

> set bgColor black

> ui mousemode right select

> select #6/B:459

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/B:460

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select #6/B:30

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select #6/B:30

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select clear

> select clear

> select clear

> select clear

> select #6

2967 atoms, 3040 bonds, 3 pseudobonds, 367 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #6,1,0,0,-94.508,0,1,0,4.0449,0,0,1,107.67

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.97409,0.19028,-0.1222,-97.99,0.14873,-0.94611,-0.28767,365.01,-0.17035,0.26204,-0.9499,479.89

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.97409,0.19028,-0.1222,-34.607,0.14873,-0.94611,-0.28767,341.34,-0.17035,0.26204,-0.9499,496.39

> view matrix models
> #6,0.97409,0.19028,-0.1222,14.241,0.14873,-0.94611,-0.28767,404.43,-0.17035,0.26204,-0.9499,488.54

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.88083,-0.11275,0.45981,-24.642,0.25029,-0.71349,-0.65443,411.86,0.40185,0.69153,-0.60024,214.58

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.88083,-0.11275,0.45981,-36.228,0.25029,-0.71349,-0.65443,436.15,0.40185,0.69153,-0.60024,219.86

> view matrix models
> #6,0.88083,-0.11275,0.45981,-50.392,0.25029,-0.71349,-0.65443,395.89,0.40185,0.69153,-0.60024,192.63

> view matrix models
> #6,0.88083,-0.11275,0.45981,-48.631,0.25029,-0.71349,-0.65443,418.77,0.40185,0.69153,-0.60024,173.38

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.64439,-0.76461,0.011298,501.76,-0.54415,0.44811,-0.7093,409.11,0.53727,-0.46321,-0.70482,363.9

> hide #4 models

> hide #3.1 models

> hide #!2 models

> view matrix models
> #6,-0.48153,-0.87362,-0.070063,499.23,-0.59058,0.38251,-0.71056,431.43,0.64756,-0.30078,-0.70014,309.4

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.48153,-0.87362,-0.070063,490.33,-0.59058,0.38251,-0.71056,425.17,0.64756,-0.30078,-0.70014,310.57

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.98972,0.059401,0.13007,-48.44,0.11729,-0.85758,-0.50079,438.26,0.0818,0.5109,-0.85574,329.03

Opened dmSer_monomer.pdb map 10 as #7, grid size 34,37,38, pixel 3.33, shown
at level 0.0589, step 1, values float32  
Fit map dmSer_monomer.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip
using 2124 points  
correlation = 0.9127, correlation about mean = 0.221, overlap = 201.5  
steps = 256, shift = 13.1, angle = 64.2 degrees  
  
Position of dmSer_monomer.pdb map 10 (#7) relative to
cryosparc_P64_J567_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
-0.41172816 -0.83849172 0.35694756 361.44582445  
0.63423323 0.01761232 0.77294115 -80.08988683  
-0.65439143 0.54462964 0.52454782 129.12273817  
Axis -0.12676441 0.56152135 0.81769466  
Axis point 224.65711033 55.05861868 0.00000000  
Rotation angle (degrees) 115.77155115  
Shift along axis 14.79232778  
  
Average map value = 0.4026 for 2967 atoms, 1351 outside contour  

> view matrix models
> #6,0.89961,0.38657,-0.20313,-19.236,0.16105,-0.72607,-0.66849,426.59,-0.40591,0.56867,-0.71544,398.8

> volume #1 level 0.3129

> close #1

> volume #5 level 0.5707

> volume #5 level 0.4215

> view matrix models
> #6,0.84409,0.52927,-0.085876,-54.16,0.1063,-0.32215,-0.9407,421.63,-0.52555,0.78491,-0.32819,313.3

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.84409,0.52927,-0.085876,-45.545,0.1063,-0.32215,-0.9407,444.12,-0.52555,0.78491,-0.32819,312.87

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.45272,-0.84137,-0.29521,323.72,-0.54073,0.0041952,-0.84118,516.24,0.70898,0.54045,-0.45305,96.724

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.45272,-0.84137,-0.29521,313.25,-0.54073,0.0041952,-0.84118,508.16,0.70898,0.54045,-0.45305,90.555

> view matrix models
> #6,0.45272,-0.84137,-0.29521,311.75,-0.54073,0.0041952,-0.84118,512.3,0.70898,0.54045,-0.45305,95.862

> view matrix models
> #6,0.45272,-0.84137,-0.29521,320.25,-0.54073,0.0041952,-0.84118,516.66,0.70898,0.54045,-0.45305,93.974

> ui mousemode right "rotate selected models"

> view matrix models
> #6,-0.36245,0.75023,-0.55298,279.82,0.72194,-0.14925,-0.67567,221.79,-0.58944,-0.64411,-0.48752,604.77

> view matrix models
> #6,-0.34339,0.89058,-0.29824,201.5,0.72617,0.050376,-0.68567,187.97,-0.59562,-0.45202,-0.66401,607

> ui mousemode right "translate selected models"

> view matrix models
> #6,-0.34339,0.89058,-0.29824,200.2,0.72617,0.050376,-0.68567,185.41,-0.59562,-0.45202,-0.66401,610.03

> view matrix models
> #6,-0.34339,0.89058,-0.29824,197.96,0.72617,0.050376,-0.68567,185.19,-0.59562,-0.45202,-0.66401,610.34

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.20172,0.93302,-0.29796,65.543,0.81466,-0.32872,-0.47778,190.58,-0.54373,-0.14636,-0.8264,576.72

Fit molecule dmSer_monomer.pdb (#6) to map cryosparc_P64_J567_map.mrc z flip
(#5) using 2967 atoms  
average map value = 0.4029, steps = 144  
shifted from previous position = 19.2  
rotated from previous position = 35.6 degrees  
atoms outside contour = 1788, contour level = 0.42147  
  
Position of dmSer_monomer.pdb (#6) relative to cryosparc_P64_J567_map.mrc z
flip (#5) coordinates:  
Matrix rotation and translation  
0.88707098 0.42222441 -0.18663237 -49.03411228  
-0.43050774 0.61070172 -0.66461004 336.46864139  
-0.16663787 0.66990295 0.72350664 -42.22229793  
Axis 0.84259283 -0.01262424 -0.53840315  
Axis point 0.00000000 233.66118265 368.96301673  
Rotation angle (degrees) 52.36423052  
Shift along axis -22.83083530  
  

> show #4 models

> show #!2 models

> hide #!5 models

> ui mousemode right "translate selected models"

> view matrix models
> #6,0.026928,0.67982,-0.73288,236.15,0.94316,-0.26022,-0.20673,80.29,-0.33125,-0.68566,-0.64819,594.53

> ui mousemode right "rotate selected models"

> view matrix models
> #6,0.86552,0.49493,-0.076951,-51.307,0.47174,-0.85712,-0.2069,292.42,-0.16836,0.14277,-0.97533,476.36

> show #!5 models

> view matrix models
> #6,0.26069,0.95399,-0.14812,21.168,0.92172,-0.29158,-0.25574,100.19,-0.28717,-0.069857,-0.95533,536.77

> ~select #6

Nothing selected  

> close #6-7

> open /Users/joanapaulino/Downloads/AF-Q86VE9-F1-model_v2.pdb

AF-Q86VE9-F1-model_v2.pdb title:  
Alphafold monomer V2.0 prediction for serine incorporator 5 (Q86VE9) [more
info...]  
  
Chain information for AF-Q86VE9-F1-model_v2.pdb #1  
---  
Chain | Description  
A | serine incorporator 5  
  

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,-28.552,0,1,0,95.1,0,0,1,344.87

> view matrix models #1,1,0,0,171.29,0,1,0,192.55,0,0,1,298.24

> ui mousemode right select

> ~select #1

Nothing selected  

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> ~select #1

Nothing selected  

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> ~select #1

Nothing selected  

> select clear

> select clear

> select clear

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right select

> select clear

> select clear

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> select #1/A:422

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> view matrix models #1,1,0,0,142.67,0,1,0,185.31,0,0,1,319

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.98562,0.1197,-0.11929,142.11,-0.14272,0.9676,-0.20827,186.44,0.090495,0.2223,0.97077,317.19

> view matrix models
> #1,0.98548,0.12095,-0.11914,142.1,-0.14404,0.96709,-0.20973,186.45,0.089852,0.22385,0.97047,317.18

> ui mousemode right select

> select #1/A:345

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select clear

> select #1/A:389

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:389

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui mousemode right "translate selected models"

> select #1

3289 atoms, 3371 bonds, 423 residues, 1 model selected  

> view matrix models
> #1,0.98548,0.12095,-0.11914,197.44,-0.14404,0.96709,-0.20973,220.55,0.089852,0.22385,0.97047,275.16

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.9161,0.40049,-0.019236,198.55,-0.39597,-0.89612,0.20045,234.28,0.063039,0.19124,0.97952,275.43

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.9161,0.40049,-0.019236,208.59,-0.39597,-0.89612,0.20045,227.41,0.063039,0.19124,0.97952,264.33

Fit molecule AF-Q86VE9-F1-model_v2.pdb (#1) to map cryosparc_P64_J567_map.mrc
z flip (#5) using 3289 atoms  
average map value = 0.3863, steps = 260  
shifted from previous position = 14.9  
rotated from previous position = 32.5 degrees  
atoms outside contour = 2188, contour level = 0.42147  
  
Position of AF-Q86VE9-F1-model_v2.pdb (#1) relative to
cryosparc_P64_J567_map.mrc z flip (#5) coordinates:  
Matrix rotation and translation  
-0.79777253 -0.56951509 0.19801906 195.05644723  
-0.50913117 0.81220747 0.28478849 214.44406485  
-0.32302390 0.12637876 -0.93791469 174.16072666  
Axis -0.28910658 0.95093242 0.11020402  
Axis point 141.56576331 0.00000000 56.79200727  
Rotation angle (degrees) 164.09970069  
Shift along axis 166.72292314  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.90964,-0.2753,-0.31107,218.16,0.31088,-0.04552,0.94936,204.77,-0.27552,-0.96028,0.044179,277.88

> ui mousemode right "translate selected models"

> view matrix models
> #1,0.90964,-0.2753,-0.31107,216.99,0.31088,-0.04552,0.94936,208.65,-0.27552,-0.96028,0.044179,282.21

> view matrix models
> #1,0.90964,-0.2753,-0.31107,215.19,0.31088,-0.04552,0.94936,211.02,-0.27552,-0.96028,0.044179,284.96

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.91229,0.32269,-0.25218,213.8,-0.39329,-0.86201,0.31977,220.51,-0.11419,0.3909,0.91332,271.64

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.91229,0.32269,-0.25218,210.76,-0.39329,-0.86201,0.31977,216.51,-0.11419,0.3909,0.91332,268.27

> view matrix models
> #1,-0.91229,0.32269,-0.25218,211.45,-0.39329,-0.86201,0.31977,216.46,-0.11419,0.3909,0.91332,268.11

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.8971,0.18256,-0.40234,212.95,-0.33985,-0.86703,0.36436,216.27,-0.28232,0.4636,0.83986,268.08

> view matrix models
> #1,-0.89927,0.37458,-0.22584,210.95,-0.43546,-0.81532,0.38162,216,-0.041188,0.44152,0.89631,267.63

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.89927,0.37458,-0.22584,218.7,-0.43546,-0.81532,0.38162,220.31,-0.041188,0.44152,0.89631,264.4

> view matrix models
> #1,-0.89927,0.37458,-0.22584,217.56,-0.43546,-0.81532,0.38162,220.67,-0.041188,0.44152,0.89631,264.27

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.95757,0.23018,-0.17345,218.64,-0.26541,-0.93885,0.21937,221.78,-0.11235,0.25609,0.9601,265.66

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.95757,0.23018,-0.17345,214.15,-0.26541,-0.93885,0.21937,219.72,-0.11235,0.25609,0.9601,265.84

> ~select #1

Nothing selected  

> volume #5 level 0.238

> ui tool show "Side View"

> volume #5 level 0.3876

> hide #!5 models

> show #!5 models

> volume #5 level 0.1819

> volume #5 level 0.3783

> volume #5 level 0.2941

> save
> /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/chX_session_serinc5WTAP2Nef_GOKrios.cxs
> includeMaps true

> close session

> open
> /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_00_02800_volume.mrc

Opened cryosparc_P73_J25_class_00_02800_volume.mrc as #1, grid size 48,48,48,
pixel 5.31, shown at level 0.692, step 1, values float32  

> surface dust #1 size 53.1

> volume #1 level 0.9069

> volume #1 level 0.6444

> surface dust #1 size 53.1

> surface dust #1 size 53.1

> volume #1 level 0.7876

Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 609, in closeEvent  
sbar.destroy()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/statusbar.py", line 51, in destroy  
v.delete()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 438, in delete  
self.make_current()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 99, in make_current  
qc = self._initialize_context()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
RuntimeError: wrapped C/C++ object of type QScreen has been deleted  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 125, in _initialize_context  
qc.setScreen(self._screen)  
  
See log for complete Python traceback.  
  

> open
> /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc

Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #2, grid size 48,48,48,
pixel 5.31, shown at level 0.682, step 1, values float32  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 73, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 85, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 173, in capture_image  
self.image = models_image(session, models, size)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 235, in models_image  
image = v.image(width, height, camera = c, drawings = models)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 413, in image  
if not self._use_opengl():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 104, in _use_opengl  
if not self._render.make_current():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
Error processing trigger "frame drawn":  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
  
See log for complete Python traceback.  
  

> open
> /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc

Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #3, grid size 48,48,48,
pixel 5.31, shown at level 0.682, step 1, values float32  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 73, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 85, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 173, in capture_image  
self.image = models_image(session, models, size)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 235, in models_image  
image = v.image(width, height, camera = c, drawings = models)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 413, in image  
if not self._use_opengl():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 104, in _use_opengl  
if not self._render.make_current():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
Error processing trigger "frame drawn":  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
  
See log for complete Python traceback.  
  

> open
> /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc

Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #4, grid size 48,48,48,
pixel 5.31, shown at level 0.682, step 1, values float32  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 73, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 85, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 173, in capture_image  
self.image = models_image(session, models, size)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 235, in models_image  
image = v.image(width, height, camera = c, drawings = models)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 413, in image  
if not self._use_opengl():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 104, in _use_opengl  
if not self._render.make_current():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
Error processing trigger "frame drawn":  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
  
See log for complete Python traceback.  
  

> open
> /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc

Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #5, grid size 48,48,48,
pixel 5.31, shown at level 0.682, step 1, values float32  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 73, in <lambda>  
t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb())  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 85, in capture_thumbnails_cb  
fs.capture_image(models, ses)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 173, in capture_image  
self.image = models_image(session, models, size)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/filehistory.py", line 235, in models_image  
image = v.image(width, height, camera = c, drawings = models)  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 413, in image  
if not self._use_opengl():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/view.py", line 104, in _use_opengl  
if not self._render.make_current():  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 478, in make_current  
return self._opengl_context.make_current()  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
Error processing trigger "frame drawn":  
chimerax.graphics.opengl.OpenGLError: Could not make graphics context current  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/graphics/opengl.py", line 108, in make_current  
raise OpenGLError("Could not make graphics context current")  
  
See log for complete Python traceback.  
  




OpenGL version: unknown
Could not make opengl context currentHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1037.147.1.0.0 (iBridge: 17.16.16065.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G73)
      Kernel Version: Darwin 19.6.0
      Time since boot: 7 days 6:41

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.01.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: YMYH14BR3UKL
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Adapter Type: DVI or HDMI
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-Phenix: 0.3
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

[pett]

Reported by Joana Paulino

[Tom Goddard]

This was fixed more than a year ago. The error happens when using two screens, starting ChimeraX on one screen, then disconnecting that screen, and then using ChimeraX on the remaining screen. Get the current ChimeraX 1.4 which does not have this error.