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Opened 8 hours ago
#20474 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: macOS-26.3-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/a13583/Desktop/PPL/AF3/fold_ppl_6xhis/fold_ppl_6xhis_model_0.cif
Chain information for fold_ppl_6xhis_model_0.cif #1
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/a13583/Desktop/PPL/AF3/fold_ppl_dimer_6his/fold_ppl_dimer_6his_model_0.cif
Chain information for fold_ppl_dimer_6his_model_0.cif #2
---
Chain | Description
A B | .
Computing secondary structure
> open
> /Users/a13583/Desktop/PPL/AF3/ppl_d10a_monomer/fold_ppl_d10a_monomer_model_0.cif
Chain information for fold_ppl_d10a_monomer_model_0.cif #3
---
Chain | Description
A | .
Computing secondary structure
> hide #1 models
> hide #2 models
> set bgColor white
> set bgColor #ffffff00
> open
> /Users/a13583/Desktop/PPL/AF3/ppl_d10a_dimer/fold_ppl_d10a_dimer_model_0.cif
Chain information for fold_ppl_d10a_dimer_model_0.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> hide #3 models
> show #2 models
> select add #2
14164 atoms, 14470 bonds, 1798 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,5.1154,0,1,0,7.0987,0,0,1,5.4499
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.90503,-0.41605,-0.088486,6.0161,0.1991,0.5982,-0.77622,6.2716,0.37588,0.68488,0.62422,2.6863
> view matrix models
> #2,0.9204,-0.31412,-0.23281,5.5101,0.16212,0.84844,-0.50385,6.2711,0.35579,0.426,0.83183,3.6564
> view matrix models
> #2,0.62953,-0.75365,-0.18897,7.008,0.65076,0.64431,-0.40171,6.1311,0.4245,0.12991,0.89606,4.3109
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.62953,-0.75365,-0.18897,6.7279,0.65076,0.64431,-0.40171,-5.0612,0.4245,0.12991,0.89606,-4.0267
> view matrix models
> #2,0.62953,-0.75365,-0.18897,19.067,0.65076,0.64431,-0.40171,2.6911,0.4245,0.12991,0.89606,-20.895
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.95273,0.0089604,-0.30369,16.685,0.2123,0.6954,0.68654,5.2217,0.21734,-0.71856,0.66063,-19.135
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.95273,0.0089604,-0.30369,9.4594,0.2123,0.6954,0.68654,-6.3164,0.21734,-0.71856,0.66063,-3.5987
> view matrix models
> #2,0.95273,0.0089604,-0.30369,-6.1573,0.2123,0.6954,0.68654,-2.2094,0.21734,-0.71856,0.66063,10.368
> view matrix models
> #2,0.95273,0.0089604,-0.30369,-10.032,0.2123,0.6954,0.68654,7.041,0.21734,-0.71856,0.66063,5.686
> view matrix models
> #2,0.95273,0.0089604,-0.30369,-18.829,0.2123,0.6954,0.68654,19.057,0.21734,-0.71856,0.66063,2.672
> view matrix models
> #2,0.95273,0.0089604,-0.30369,-11.132,0.2123,0.6954,0.68654,7.2166,0.21734,-0.71856,0.66063,3.3835
> view matrix models
> #2,0.95273,0.0089604,-0.30369,-10.421,0.2123,0.6954,0.68654,6.6164,0.21734,-0.71856,0.66063,4.482
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.95927,-0.0050832,-0.28245,-10.363,0.20608,0.69649,0.68734,6.6253,0.19323,-0.71755,0.66917,4.5331
> view matrix models
> #2,0.94288,-0.018589,-0.33262,-10.397,0.24443,0.71698,0.65283,6.4581,0.22635,-0.69684,0.68057,4.4561
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-10.306,0.31902,0.65603,0.68399,6.5299,0.1864,-0.75104,0.6334,4.5529
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-9.641,0.31902,0.65603,0.68399,4.6266,0.1864,-0.75104,0.6334,3.5486
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-8.7995,0.31902,0.65603,0.68399,2.921,0.1864,-0.75104,0.6334,4.6157
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-10.22,0.31902,0.65603,0.68399,4.1816,0.1864,-0.75104,0.6334,4.7178
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-10.282,0.31902,0.65603,0.68399,5.1869,0.1864,-0.75104,0.6334,2.5225
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-10.268,0.31902,0.65603,0.68399,5.0313,0.1864,-0.75104,0.6334,1.9885
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-9.0856,0.31902,0.65603,0.68399,3.2571,0.1864,-0.75104,0.6334,3.55
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.
> transparent #2
Unknown command: transparent #2
> transparency #2
Missing or invalid "percent" argument: Expected a number
> transparency *2
Missing or invalid "percent" argument: Expected a number
> transparency 2
> transparency #2 80
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-8.5483,0.31902,0.65603,0.68399,3.3472,0.1864,-0.75104,0.6334,3.9443
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-9.0643,0.31902,0.65603,0.68399,5.3629,0.1864,-0.75104,0.6334,3.6105
> select subtract #2
Nothing selected
> select add #2
14164 atoms, 14470 bonds, 1798 residues, 1 model selected
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show sel surfaces
> transparency sel 50
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-8.4613,0.31902,0.65603,0.68399,5.888,0.1864,-0.75104,0.6334,3.3427
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-5.2708,0.31902,0.65603,0.68399,-0.059056,0.1864,-0.75104,0.6334,3.8615
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-4.4172,0.31902,0.65603,0.68399,0.80025,0.1864,-0.75104,0.6334,3.9056
> hide sel surfaces
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-6.793,0.31902,0.65603,0.68399,3.3023,0.1864,-0.75104,0.6334,7.1355
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-7.8962,0.31902,0.65603,0.68399,5.9295,0.1864,-0.75104,0.6334,5.7999
> view matrix models
> #2,0.92924,-0.074569,-0.36188,-7.7965,0.31902,0.65603,0.68399,5.8965,0.1864,-0.75104,0.6334,5.0564
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.94305,-0.098723,-0.31766,-7.6862,0.30362,0.64558,0.70074,5.9737,0.1359,-0.75729,0.63879,5.1592
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.94305,-0.098723,-0.31766,-7.8621,0.30362,0.64558,0.70074,6.6765,0.1359,-0.75729,0.63879,5.4374
> hide #4 models
> close #4
> close #3
> hide #!2 models
> select subtract #2
2 models selected
> show #!2 models
> open
> /Users/a13583/Desktop/PPL/AF3/ppl_d10a_dimer/fold_ppl_d10a_dimer_model_0.cif
Chain information for fold_ppl_d10a_dimer_model_0.cif #3
---
Chain | Description
A B | .
Computing secondary structure
> select add #3
14148 atoms, 14452 bonds, 1798 residues, 1 model selected
> view matrix models #3,1,0,0,2.7883,0,1,0,13.704,0,0,1,-56.861
> view matrix models #3,1,0,0,1.4987,0,1,0,14.39,0,0,1,-83.612
> open
> /Users/a13583/Desktop/PPL/AF3/ppl_h14a_dimer/fold_ppl_h14a_dimer_model_0.cif
Chain information for fold_ppl_h14a_dimer_model_0.cif #4
---
Chain | Description
A B | .
Computing secondary structure
> hide #3 models
> select subtract #3
Nothing selected
> select add #4
14148 atoms, 14452 bonds, 1798 residues, 1 model selected
> view matrix models #4,1,0,0,-1.1731,0,1,0,-3.6206,0,0,1,-74.203
> view matrix models #4,1,0,0,0.7422,0,1,0,0.32477,0,0,1,-0.55423
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.81916,-0.54972,0.16365,1.3816,0.36983,0.28816,-0.88328,6.6369,0.4384,0.78407,0.43936,0.17232
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.81916,-0.54972,0.16365,-5.7767,0.36983,0.28816,-0.88328,3.7764,0.4384,0.78407,0.43936,12.086
> view matrix models
> #4,0.81916,-0.54972,0.16365,-10.029,0.36983,0.28816,-0.88328,11.156,0.4384,0.78407,0.43936,13.122
> view matrix models
> #4,0.81916,-0.54972,0.16365,-8.1139,0.36983,0.28816,-0.88328,11.692,0.4384,0.78407,0.43936,14.261
> view matrix models
> #4,0.81916,-0.54972,0.16365,-10.795,0.36983,0.28816,-0.88328,19.217,0.4384,0.78407,0.43936,13.003
> view matrix models
> #4,0.81916,-0.54972,0.16365,-12.236,0.36983,0.28816,-0.88328,17.673,0.4384,0.78407,0.43936,11.246
> view matrix models
> #4,0.81916,-0.54972,0.16365,-12.139,0.36983,0.28816,-0.88328,19.523,0.4384,0.78407,0.43936,11.117
> view matrix models
> #4,0.81916,-0.54972,0.16365,-14.2,0.36983,0.28816,-0.88328,18.627,0.4384,0.78407,0.43936,11.381
> view matrix models
> #4,0.81916,-0.54972,0.16365,-10.622,0.36983,0.28816,-0.88328,20.037,0.4384,0.78407,0.43936,8.4234
> view matrix models
> #4,0.81916,-0.54972,0.16365,-13.509,0.36983,0.28816,-0.88328,20.225,0.4384,0.78407,0.43936,8.4009
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.72347,-0.45573,0.51856,-15.562,0.57373,-0.020864,-0.81878,20.633,0.38396,0.88987,0.24637,9.1411
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.72347,-0.45573,0.51856,-9.2725,0.57373,-0.020864,-0.81878,19.353,0.38396,0.88987,0.24637,3.243
> view matrix models
> #4,0.72347,-0.45573,0.51856,-7.2265,0.57373,-0.020864,-0.81878,13.177,0.38396,0.88987,0.24637,4.1109
> view matrix models
> #4,0.72347,-0.45573,0.51856,-7.6267,0.57373,-0.020864,-0.81878,16.396,0.38396,0.88987,0.24637,2.1493
> view matrix models
> #4,0.72347,-0.45573,0.51856,-7.6606,0.57373,-0.020864,-0.81878,16.407,0.38396,0.88987,0.24637,2.1058
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.722,-0.36877,0.58543,-8.2327,0.58429,-0.12822,-0.80135,16.593,0.37057,0.92064,0.1229,2.669
> view matrix models
> #4,0.72117,-0.36429,0.58925,-8.2639,0.58526,-0.13472,-0.79957,16.6,0.37066,0.92149,0.11605,2.7022
> view matrix models
> #4,0.74233,-0.39806,0.53897,-7.9222,0.51645,-0.17254,-0.83875,16.923,0.42687,0.90099,0.0775,2.9379
> view matrix models
> #4,0.70878,-0.46957,0.52644,-7.6609,0.52985,-0.1383,-0.83674,16.819,0.46572,0.87199,0.15078,2.6222
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.70878,-0.46957,0.52644,-7.101,0.52985,-0.1383,-0.83674,7.761,0.46572,0.87199,0.15078,7.5012
> view matrix models
> #4,0.70878,-0.46957,0.52644,-5.2524,0.52985,-0.1383,-0.83674,5.415,0.46572,0.87199,0.15078,6.7334
> view matrix models
> #4,0.70878,-0.46957,0.52644,-5.0152,0.52985,-0.1383,-0.83674,5.7769,0.46572,0.87199,0.15078,7.0003
> view matrix models
> #4,0.70878,-0.46957,0.52644,-4.9869,0.52985,-0.1383,-0.83674,5.7975,0.46572,0.87199,0.15078,7.0197
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.69423,-0.51688,0.50088,-4.727,0.50575,-0.14483,-0.85043,5.8928,0.51211,0.84372,0.16087,7.0269
> view matrix models
> #4,0.69366,-0.51915,0.49931,-4.7128,0.50483,-0.14406,-0.85111,5.8946,0.51379,0.84245,0.16215,7.0231
> view matrix models
> #4,0.80272,-0.40882,0.43417,-4.6962,0.45165,-0.058652,-0.89026,5.8912,0.38942,0.91073,0.13756,7.0106
> view matrix models
> #4,0.75932,-0.40107,0.51242,-5.1081,0.53561,-0.061959,-0.84219,5.6252,0.36953,0.91395,0.16777,6.852
> view matrix models
> #4,0.80458,-0.40056,0.4384,-4.7402,0.45021,-0.069966,-0.89018,5.9206,0.38724,0.91359,0.12404,7.0738
> view matrix models
> #4,0.80129,-0.42968,0.41629,-4.5489,0.41725,-0.097313,-0.90357,6.0712,0.42876,0.89772,0.10131,7.2201
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.80129,-0.42968,0.41629,-7.4268,0.41725,-0.097313,-0.90357,5.525,0.42876,0.89772,0.10131,7.3306
> view matrix models
> #4,0.80129,-0.42968,0.41629,-6.5542,0.41725,-0.097313,-0.90357,4.222,0.42876,0.89772,0.10131,10.786
> view matrix models
> #4,0.80129,-0.42968,0.41629,-5.7102,0.41725,-0.097313,-0.90357,0.97773,0.42876,0.89772,0.10131,10.529
> view matrix models
> #4,0.80129,-0.42968,0.41629,-7.5051,0.41725,-0.097313,-0.90357,1.4661,0.42876,0.89772,0.10131,9.6486
> view matrix models
> #4,0.80129,-0.42968,0.41629,-8.1463,0.41725,-0.097313,-0.90357,0.82526,0.42876,0.89772,0.10131,8.8299
> view matrix models
> #4,0.80129,-0.42968,0.41629,-8.5876,0.41725,-0.097313,-0.90357,0.55057,0.42876,0.89772,0.10131,8.7687
> view matrix models
> #4,0.80129,-0.42968,0.41629,-7.5544,0.41725,-0.097313,-0.90357,-0.015747,0.42876,0.89772,0.10131,9.3622
> select subtract #4
Nothing selected
> hide #4 models
> open
> /Users/a13583/Desktop/PPL/AF3/ppl_h48a_dimer/fold_ppl_h48a_dimer_model_0.cif
Chain information for fold_ppl_h48a_dimer_model_0.cif #5
---
Chain | Description
A B | .
Computing secondary structure
> select add #5
14148 atoms, 14452 bonds, 1798 residues, 1 model selected
> view matrix models #5,1,0,0,-21.492,0,1,0,-15.764,0,0,1,-5.0931
> view matrix models #5,1,0,0,-26.918,0,1,0,-20.494,0,0,1,-4.8588
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.34536,-0.91844,0.19283,-26.122,0.76074,0.15366,-0.63061,-17.702,0.54955,0.36448,0.75176,-4.7376
> view matrix models
> #5,-0.0036486,-0.4149,0.90986,-28.032,0.92402,0.34648,0.1617,-18.682,-0.38233,0.84132,0.38211,-6.0416
> view matrix models
> #5,0.12931,-0.93625,0.32667,-26.423,0.68979,0.3216,0.64867,-19.343,-0.71237,0.14146,0.6874,-5.4398
> view matrix models
> #5,0.090769,-0.90302,0.41989,-26.609,0.74909,0.33974,0.56872,-19.24,-0.65622,0.26291,0.70728,-5.6185
> view matrix models
> #5,0.091106,-0.90219,0.42161,-26.612,0.74931,0.34096,0.5677,-19.24,-0.65592,0.26419,0.70708,-5.6203
> view matrix models
> #5,0.37822,-0.65584,0.65332,-27.009,0.4436,0.74784,0.49392,-20.149,-0.81251,0.103,0.57377,-5.3506
> view matrix models
> #5,0.23015,-0.69146,0.68477,-27.114,0.36242,0.71394,0.59911,-20.27,-0.90315,0.11029,0.41491,-5.2863
> ui mousemode right "translate selected models"
> view matrix models
> #5,0.23015,-0.69146,0.68477,0.44246,0.36242,0.71394,0.59911,-0.87091,-0.90315,0.11029,0.41491,2.8885
> view matrix models
> #5,0.23015,-0.69146,0.68477,-4.4661,0.36242,0.71394,0.59911,0.79124,-0.90315,0.11029,0.41491,6.0968
> view matrix models
> #5,0.23015,-0.69146,0.68477,-2.3172,0.36242,0.71394,0.59911,4.4684,-0.90315,0.11029,0.41491,3.5915
> view matrix models
> #5,0.23015,-0.69146,0.68477,-3.7083,0.36242,0.71394,0.59911,5.1785,-0.90315,0.11029,0.41491,5.9065
> view matrix models
> #5,0.23015,-0.69146,0.68477,-3.7588,0.36242,0.71394,0.59911,5.3907,-0.90315,0.11029,0.41491,3.7616
> view matrix models
> #5,0.23015,-0.69146,0.68477,-3.7812,0.36242,0.71394,0.59911,5.3719,-0.90315,0.11029,0.41491,3.8068
> select subtract #5
Nothing selected
> hide #5 models
> show #3 models
> select add #3
14148 atoms, 14452 bonds, 1798 residues, 1 model selected
> view matrix models #3,1,0,0,-9.5651,0,1,0,1.7738,0,0,1,-82.108
> view matrix models #3,1,0,0,-16.819,0,1,0,-3.1414,0,0,1,-91.676
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.4133,-0.43654,0.79913,-28.827,0.41224,-0.69281,-0.59167,-20.953,0.81194,0.57397,-0.10638,-75.453
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.4133,-0.43654,0.79913,-76.939,0.41224,-0.69281,-0.59167,-66.716,0.81194,0.57397,-0.10638,-97.53
> select subtract #3
Nothing selected
> open
> /Users/a13583/Desktop/PPL/AF3/ppl_h12a_dimer/fold_ppl_h12a_dimer_model_1.cif
Chain information for fold_ppl_h12a_dimer_model_1.cif #6
---
Chain | Description
A B | .
Computing secondary structure
> hide #3 models
> select add #6
14154 atoms, 14458 bonds, 1798 residues, 1 model selected
> view matrix models #6,1,0,0,-70.658,0,1,0,-47.38,0,0,1,-95.715
> view matrix models #6,1,0,0,-63.997,0,1,0,-43.822,0,0,1,-83.846
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.20463,-0.90089,0.38279,-81.458,0.94978,-0.27732,-0.14494,-78.695,0.23672,0.33391,0.9124,-76.576
> view matrix models
> #6,-0.20949,-0.87665,0.43313,-79.716,0.95888,-0.27092,-0.084578,-77.172,0.19149,0.3976,0.89736,-75.327
> view matrix models
> #6,-0.22823,-0.81469,0.53309,-75.912,0.96893,-0.24366,0.042458,-73.621,0.095302,0.52622,0.84499,-73.301
> view matrix models
> #6,-0.22796,-0.81548,0.53201,-75.956,0.96889,-0.24408,0.041027,-73.664,0.096394,0.52481,0.84575,-73.319
> view matrix models
> #6,-0.33238,-0.8062,0.48945,-76.858,0.9399,-0.32617,0.10101,-74.543,0.07821,0.49361,0.86616,-73.719
> hide #!2 models
> select subtract #6
Nothing selected
Traceback (most recent call last):
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/2HNH.cif
Summary of feedback from opening /Users/a13583/Downloads/2HNH.cif
---
notes | PDBx/mmCIF styling lost on line 4136. Rereading mmCIF file from the beginning.
Fetching CCD PO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif
2HNH.cif title:
Crystal structure of the catalytic α subunit of E. coli replicative DNA
polymerase III [more info...]
Chain information for 2HNH.cif #7
---
Chain | Description | UniProt
A | DNA polymerase III alpha subunit | DPO3A_ECOLI 1-910
Non-standard residues in 2HNH.cif #7
---
PO4 — phosphate ion
60 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> open /Users/a13583/Downloads/2HNH.cif
Summary of feedback from opening /Users/a13583/Downloads/2HNH.cif
---
note | PDBx/mmCIF styling lost on line 4136. Rereading mmCIF file from the beginning.
2HNH.cif title:
Crystal structure of the catalytic α subunit of E. coli replicative DNA
polymerase III [more info...]
Chain information for 2HNH.cif #8
---
Chain | Description | UniProt
A | DNA polymerase III alpha subunit | DPO3A_ECOLI 1-910
Non-standard residues in 2HNH.cif #8
---
PO4 — phosphate ion
60 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> close #8
> hide #6 models
> show #1 models
> select add #7
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> view matrix models
> #7,-0.11337,0.66517,0.73804,-20.157,0.22514,-0.7063,0.67115,27.207,0.96771,0.24226,-0.069681,5.4462
> view matrix models
> #7,0.46028,-0.51172,-0.72546,-18.875,-0.85957,-0.46122,-0.22004,-12.131,-0.222,0.72486,-0.65215,-33.715
> view matrix models
> #7,0.79436,-0.52568,-0.30438,-5.1488,0.59224,0.78165,0.19564,18.005,0.13507,-0.33567,0.93224,4.6307
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.79436,-0.52568,-0.30438,5.2051,0.59224,0.78165,0.19564,30.106,0.13507,-0.33567,0.93224,65.822
> view matrix models
> #7,0.79436,-0.52568,-0.30438,6.1623,0.59224,0.78165,0.19564,37.035,0.13507,-0.33567,0.93224,67.538
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.14529,0.62014,-0.77092,-23.8,0.59435,0.56822,0.5691,43.914,0.79098,-0.54088,-0.28602,67.007
> view matrix models
> #7,-0.46088,0.7477,0.47805,-21.119,0.1585,-0.46066,0.87331,45.738,0.87319,0.47827,0.093801,66.739
> view matrix models
> #7,-0.26194,-0.88139,0.39312,-5.7286,0.93091,-0.1233,0.34382,53.59,-0.25456,0.45601,0.85279,51.611
> view matrix models
> #7,-0.31564,-0.89553,-0.31368,-16.812,0.91121,-0.19384,-0.36349,43.698,0.26471,-0.40056,0.8772,70.228
> view matrix models
> #7,-0.055186,-0.66208,-0.74739,-18.639,-0.63191,0.60272,-0.48726,0.54079,0.77307,0.4454,-0.45164,56.996
> view matrix models
> #7,-0.31725,-0.67432,-0.66682,-23.451,-0.73201,0.62116,-0.27987,1.019,0.60292,0.39933,-0.69067,50.051
> view matrix models
> #7,-0.37264,-0.66055,-0.65178,-24.617,-0.63177,0.69504,-0.3432,1.892,0.67971,0.28389,-0.67631,52.873
> view matrix models
> #7,-0.10936,-0.78656,-0.60775,-17.004,0.36361,0.53739,-0.76092,20.101,0.92511,-0.3042,0.22723,75.579
> view matrix models
> #7,-0.10258,-0.8608,-0.4985,-14.762,0.23994,0.46493,-0.85221,16.501,0.96535,-0.20703,0.15884,74.827
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with 2HNH.cif, chain A
(#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> view matrix models
> #7,0.335,-0.91264,-0.23421,1.0685,0.79074,0.40749,-0.45682,7.2565,0.51235,-0.032164,0.85818,24.077
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with 2HNH.cif, chain A
(#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> select #7/A
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> select #7 8-173
Expected a keyword
> select #7：8-173
Expected an objects specifier or a keyword
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select ~sel & ##selected
6298 atoms, 6023 bonds, 1146 residues, 1 model selected
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select ~sel
84125 atoms, 85523 bonds, 11033 residues, 7 models selected
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> ui tool show "Selection Inspector"
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select ~sel & ##selected
6298 atoms, 6023 bonds, 1146 residues, 1 model selected
> hide #7 target m
> show #7 models
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select up
1344 atoms, 1371 bonds, 176 residues, 1 model selected
> select up
7147 atoms, 7298 bonds, 910 residues, 1 model selected
> select up
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> select up
85388 atoms, 86812 bonds, 11199 residues, 7 models selected
> select down
7561 atoms, 7310 bonds, 1312 residues, 3 models selected
> select down
7147 atoms, 7298 bonds, 910 residues, 1 model selected
> select down
1344 atoms, 1371 bonds, 176 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select up
1344 atoms, 1371 bonds, 176 residues, 1 model selected
> select up
7147 atoms, 7298 bonds, 910 residues, 1 model selected
> select up
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> select down
7147 atoms, 7298 bonds, 910 residues, 1 model selected
> select down
1344 atoms, 1371 bonds, 176 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select down
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select up
1344 atoms, 1371 bonds, 176 residues, 1 model selected
> select up
7147 atoms, 7298 bonds, 910 residues, 1 model selected
> hide #7 target m
> show #7 models
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select up
1344 atoms, 1371 bonds, 176 residues, 1 model selected
> hide #7 target m
> show #7 models
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> color sel cyan
> select add #7
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> select subtract #7
Nothing selected
> select add #7
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> unsel #7:8-173
Unknown command: unsel #7:8-173
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select ~sel & ##selected
6298 atoms, 6023 bonds, 1146 residues, 1 model selected
> hide #7 target m
> show #7 models
> cofr sel
> select #7:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select ~sel & ##selected
6298 atoms, 6023 bonds, 1146 residues, 1 model selected
> hide sel target a
> cartoon hide sel
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with 2HNH.cif, chain A
(#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> view matrix models
> #7,-0.49592,-0.53531,-0.68375,-22.903,0.2288,-0.84012,0.49178,31.449,-0.83768,0.087438,0.53911,-1.2883
> select add #7
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> transparency sel 80
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with 2HNH.cif, chain A
(#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> view matrix models
> #7,0.43539,-0.88058,-0.18713,1.65,0.80609,0.47389,-0.35447,4.7409,0.40082,0.0034904,0.91615,21.068
> view matrix models
> #7,0.35287,0.25137,-0.90128,-31.26,-0.93544,0.11625,-0.33382,-14.252,0.020864,0.96088,0.27616,-11.924
> view matrix models
> #7,0.058966,0.55932,-0.82685,-45.681,-0.99643,-0.01722,-0.082707,-12.104,-0.060498,0.82877,0.5563,-10.256
> rename #7 "DNA pol 3 PHP domain （2HNH）.cif"
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA pol 3 PHP domain
（2HNH）.cif, chain A (#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> view matrix models
> #7,0.30629,-0.91731,-0.25443,0.76585,0.78348,0.39473,-0.47994,7.118,0.54068,-0.052338,0.8396,25.354
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA pol 3 PHP domain
（2HNH）.cif, chain A (#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> ui mousemode right "translate selected models"
> view matrix models
> #7,0.34876,-0.90225,-0.2536,8.0774,0.75082,0.43092,-0.50057,-20.157,0.56092,-0.015833,0.82772,31.186
> fitmap #1 to #7
Expected a keyword
> matchmaker #1 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DNA pol 3 PHP domain （2HNH）.cif, chain A (#7) with
fold_ppl_6xhis_model_0.cif, chain A (#1), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> view matrix models
> #7,0.34876,-0.90225,-0.2536,19.49,0.75082,0.43092,-0.50057,24.267,0.56092,-0.015833,0.82772,5.0738
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA pol 3 PHP domain
（2HNH）.cif, chain A (#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> view matrix models
> #7,0.34876,-0.90225,-0.2536,7.23,0.75082,0.43092,-0.50057,-17.053,0.56092,-0.015833,0.82772,32.215
> ui tool show Matchmaker
> matchmaker #7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA pol 3 PHP domain
（2HNH）.cif, chain A (#7), sequence alignment score = 218.4
RMSD between 10 pruned atom pairs is 1.393 angstroms; (across all 628 pairs:
56.719)
> select subtract #7
Nothing selected
> hide #1,7 atoms
> surface #1,7
> transparency #1.1#7.1 50
> surface hidePatches #1,7
> select #7/A:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> show #!7 target m
> combine #7
> hide #8 models
> select #7/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
131 atoms, 134 bonds, 16 residues, 2 models selected
> select up
7147 atoms, 7298 bonds, 910 residues, 2 models selected
> hide #!1 models
Drag select of 166 residues
> select ~sel & ##selected
6298 atoms, 6023 bonds, 1146 residues, 1 model selected
> delete sel
> show #!1 models
> ui tool show Matchmaker
> matchmaker #!7 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA pol 3 PHP domain
（2HNH）.cif, chain A (#7), sequence alignment score = 28.9
RMSD between 4 pruned atom pairs is 1.334 angstroms; (across all 137 pairs:
29.169)
> show #8 models
> hide #8 models
> ui tool show Matchmaker
> matchmaker #8 to #7
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DNA pol 3 PHP domain （2HNH）.cif, chain A (#7) with copy of DNA pol
3 PHP domain （2HNH）.cif, chain A (#8), sequence alignment score = 3557.6
RMSD between 166 pruned atom pairs is 0.000 angstroms; (across all 166 pairs:
0.000)
> show #8 models
> hide #!7 models
> select add #8
7561 atoms, 7310 bonds, 1312 residues, 1 model selected
> cartoon sel
> hide #8 models
> show #!7 models
> select subtract #8
Nothing selected
> ui mousemode right zoom
> open 3au2
Summary of feedback from opening 3au2 fetched from pdb
---
notes | Fetching compressed mmCIF 3au2 from http://files.rcsb.org/download/3au2.cif
Fetching CCD CA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
Fetching CCD DGT from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/DGT/DGT.cif
Fetching CCD ZN from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif
3au2 title:
DNA polymerase X from Thermus thermophilus HB8 complexed with Ca-dGTP [more
info...]
Chain information for 3au2 #9
---
Chain | Description | UniProt
A | DNA polymerase beta family (X family) | Q5SJ64_THET8 1-575
Non-standard residues in 3au2 #9
---
CA — calcium ion
CL — chloride ion
DGT — 2'-deoxyguanosine-5'-triphosphate
ZN — zinc ion
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
5184 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #!7 models
> hide #!1,9 atoms
> open Q5SJ64 fromDatabase uniprot associate #9/A
Summary of feedback from opening Q5SJ64 fetched from uniprot
---
notes | Fetching compressed Q5SJ64 UniProt info from https://www.uniprot.org/uniprot/Q5SJ64.xml
Alignment identifier is Q5SJ64
Associated 3au2 chain A to Q5SJ64 with 0 mismatches
Opened UniProt Q5SJ64
> open Q5SJ64 fromDatabase uniprot associate #9/A
Summary of feedback from opening Q5SJ64 fetched from uniprot
---
notes | Destroying pre-existing alignment with identifier Q5SJ64
Alignment identifier is Q5SJ64
Associated 3au2 chain A to Q5SJ64 with 0 mismatches
Opened UniProt Q5SJ64
> select #9/A:1-315,339-418
3078 atoms, 3133 bonds, 395 residues, 1 model selected
> select #9/A:339-418
619 atoms, 635 bonds, 80 residues, 1 model selected
> select ~sel & ##selected
4565 atoms, 4010 bonds, 32 pseudobonds, 1126 residues, 2 models selected
> delete sel
> ui tool show Matchmaker
> matchmaker #!9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with 3au2, chain A (#9),
sequence alignment score = 67.1
RMSD between 36 pruned atom pairs is 0.971 angstroms; (across all 73 pairs:
7.309)
Traceback (most recent call last):
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/clustalw.aln
Summary of feedback from opening /Users/a13583/Downloads/clustalw.aln
---
notes | Alignment identifier is clustalw.aln
Associated fold_ppl_6xhis_model_0.cif chain A to Ppl with 0 mismatches
Associated fold_ppl_dimer_6his_model_0.cif chain A to Ppl with 0 mismatches
Associated fold_ppl_dimer_6his_model_0.cif chain B to Ppl with 0 mismatches
Associated fold_ppl_d10a_dimer_model_0.cif chain A to Ppl with 2 mismatches
Associated fold_ppl_d10a_dimer_model_0.cif chain B to Ppl with 2 mismatches
6 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment clustalw.aln
Opened 6 sequences from clustalw.aln
> open /Users/a13583/Downloads/2hnh_updated.cif
2hnh_updated.cif title:
Crystal structure of the catalytic α subunit of E. coli replicative DNA
polymerase III [more info...]
Chain information for 2hnh_updated.cif #10
---
Chain | Description | UniProt
A | DNA polymerase III alpha subunit | DPO3A_ECOLI 1-910
Non-standard residues in 2hnh_updated.cif #10
---
PO4 — phosphate ion
60 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> show #!7 models
> hide #10 models
> matchmaker #1 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3au2, chain A (#9) with fold_ppl_6xhis_model_0.cif, chain A (#1),
sequence alignment score = 67.1
RMSD between 36 pruned atom pairs is 0.971 angstroms; (across all 73 pairs:
7.309)
> matchmaker #1 to #9
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3au2, chain A (#9) with fold_ppl_6xhis_model_0.cif, chain A (#1),
sequence alignment score = 67.1
RMSD between 36 pruned atom pairs is 0.971 angstroms; (across all 73 pairs:
7.309)
> show #8 models
> hide #8 models
> select #10:8-173
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> show #10 models
> hide #!9 models
> hide #!7 models
> select ~sel & ##selected
6298 atoms, 6023 bonds, 1146 residues, 1 model selected
> delete sel
> select add #10
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> cartoon hide sel
> cartoon sel
> hide sel target a
> matchmaker #1 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hnh_updated.cif, chain A (#10) with fold_ppl_6xhis_model_0.cif,
chain A (#1), sequence alignment score = 28.9
RMSD between 4 pruned atom pairs is 1.334 angstroms; (across all 137 pairs:
29.169)
> show #!7 models
> matchmaker #7 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 2hnh_updated.cif, chain A (#10) with DNA pol 3 PHP domain
（2HNH）.cif, chain A (#7), sequence alignment score = 3566.6
RMSD between 166 pruned atom pairs is 0.000 angstroms; (across all 166 pairs:
0.000)
> close #7
> close #8
> rename #10 "DNA pol 3 PHP domain （2HNH）.cif"
> open /Users/a13583/Downloads/2hpi_updated.cif
Summary of feedback from opening /Users/a13583/Downloads/2hpi_updated.cif
---
note | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif
2hpi_updated.cif title:
Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous:
X-ray Structure of DNA Polymerase III [more info...]
Chain information for 2hpi_updated.cif #7
---
Chain | Description | UniProt
A | DNA polymerase III alpha subunit | DPO3A_THEAQ 1-1220
Non-standard residues in 2hpi_updated.cif #7
---
CL — chloride ion
MG — magnesium ion
ZN — zinc ion
2hpi_updated.cif mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| software_defined_assembly
> select subtract #10
Nothing selected
> select add #10
1263 atoms, 1287 bonds, 166 residues, 1 model selected
> select subtract #10
Nothing selected
> hide #!1 models
> select #7:9-184
1377 atoms, 1407 bonds, 1 pseudobond, 171 residues, 2 models selected
> select ~sel & ##selected
7778 atoms, 7900 bonds, 22 pseudobonds, 1000 residues, 3 models selected
> delete sel
> matchmaker #7 to #10
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DNA pol 3 PHP domain （2HNH）.cif, chain A (#10) with
2hpi_updated.cif, chain A (#7), sequence alignment score = 1452
RMSD between 140 pruned atom pairs is 1.087 angstroms; (across all 165 pairs:
2.739)
> rename #9 "DNA polymerase X from Thermus thermophilus(3au2)"
> open 3au6
Summary of feedback from opening 3au6 fetched from pdb
---
notes | Fetching compressed mmCIF 3au6 from http://files.rcsb.org/download/3au6.cif
Fetching CCD DDG from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/DDG/DDG.cif
Fetching CCD DG3 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/DG3/DG3.cif
3au6 title:
DNA polymerase X from Thermus thermophilus HB8 ternary complex with
primer/template DNA and ddGTP [more info...]
Chain information for 3au6 #8
---
Chain | Description | UniProt
A | DNA polymerase beta family (X family) | Q5SJ64_THET8 1-575
P | 5'-D(*CP*AP*GP*TP*AP*TP*(DDG))-3' |
T | 5'-D(*CP*GP*GP*CP*CP*AP*TP*AP*CP*TP*G)-3' |
Non-standard residues in 3au6 #8
---
CL — chloride ion
DG3 — 2'-3'-dideoxyguanosine-5'-triphosphate
MG — magnesium ion
SO4 — sulfate ion
ZN — zinc ion
> select #8:340-499
1257 atoms, 1288 bonds, 1 pseudobond, 158 residues, 2 models selected
> select ~sel & ##selected
3582 atoms, 3647 bonds, 27 pseudobonds, 456 residues, 4 models selected
> delete sel
> matchmaker #9 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3au6, chain A (#8) with DNA polymerase X from Thermus
thermophilus(3au2), chain A (#9), sequence alignment score = 2146.1
RMSD between 73 pruned atom pairs is 0.528 angstroms; (across all 77 pairs:
0.764)
> matchmaker #9 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 3au6, chain A (#8) with DNA polymerase X from Thermus
thermophilus(3au2), chain A (#9), sequence alignment score = 2146.1
RMSD between 73 pruned atom pairs is 0.528 angstroms; (across all 77 pairs:
0.764)
> show #!9 models
> hide #!7 models
> show #!7 models
> hide #10 models
> show #10 models
> hide #!7 models
> hide #10 models
> open 3f2b
Summary of feedback from opening 3f2b fetched from pdb
---
note | Fetching compressed mmCIF 3f2b from http://files.rcsb.org/download/3f2b.cif
3f2b title:
DNA Polymerase PolC from Geobacillus kaustophilus complex with DNA, dGTP, Mg
and Zn [more info...]
Chain information for 3f2b #11
---
Chain | Description | UniProt
A | DNA-directed DNA polymerase III alpha chain | Q5L0J3_GEOKA 228-424 618-1444
P | 5'-D(*DCP*DAP*DGP*DTP*DGP*DAP*DGP*DAP*DCP*DGP*DGP*DGP*DCP*DAP*DAP*DCP*DC)-3' |
T | 5'-D(*DAP*DTP*DAP*DAP*DCP*DGP*DGP*DTP*DTP*DGP*DCP*DCP*DCP*DGP*DTP*DCP*DTP*DCP*DAP*DCP*DTP*DG)-3' |
Non-standard residues in 3f2b #11
---
DGT — 2'-deoxyguanosine-5'-triphosphate
MG — magnesium ion
PO4 — phosphate ion
ZN — zinc ion
> hide #!8 models
> hide #!9 models
> rename #11 "DNA Polymerase PolC (3f2b)"
> select #11:118-280
389 atoms, 391 bonds, 48 residues, 1 model selected
> select ~sel & ##selected
8202 atoms, 8340 bonds, 55 pseudobonds, 1080 residues, 4 models selected
> delete sel
> matchmaker #9 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DNA Polymerase PolC (3f2b), chain A (#11) with DNA polymerase X
from Thermus thermophilus(3au2), chain A (#9), sequence alignment score = 4.5
RMSD between 4 pruned atom pairs is 1.243 angstroms; (across all 23 pairs:
10.217)
> show #!9 models
> matchmaker #1 to #11
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker DNA Polymerase PolC (3f2b), chain A (#11) with
fold_ppl_6xhis_model_0.cif, chain A (#1), sequence alignment score = 8.4
Fewer than 3 residues aligned; cannot match DNA Polymerase PolC (3f2b), chain
A with fold_ppl_6xhis_model_0.cif, chain A
> matchmaker #11 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA Polymerase PolC
(3f2b), chain A (#11), sequence alignment score = 8.4
Fewer than 3 residues aligned; cannot match fold_ppl_6xhis_model_0.cif, chain
A with DNA Polymerase PolC (3f2b), chain A
> hide #!9 models
> hide #!11 models
> show #!9 models
> show #!1 models
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with DNA polymerase X from
Thermus thermophilus(3au2), chain A (#9), sequence alignment score = 67.1
RMSD between 36 pruned atom pairs is 0.971 angstroms; (across all 73 pairs:
7.309)
> open /Users/a13583/Downloads/AF-A0A8J6TIP3-F1-model_v6.cif
Chain information for AF-A0A8J6TIP3-F1-model_v6.cif #12
---
Chain | Description | UniProt
A | Histidinol phosphate phosphatase domain-containing protein | A0A8J6TIP3_9BACT 1-211
Color AF-A0A8J6TIP3-F1-model_v6.cif by residue attribute pLDDT_score
> matchmaker #12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_ppl_6xhis_model_0.cif, chain A (#1) with
AF-A0A8J6TIP3-F1-model_v6.cif, chain A (#12), sequence alignment score = 151.1
RMSD between 48 pruned atom pairs is 0.798 angstroms; (across all 195 pairs:
11.290)
> hide #!9 models
> rename #12 "Polymerase/histidinol phosphatase N-terminal domain-containing
> protein(af)_v6.cif"
Traceback (most recent call last):
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> show #!2 models
> hide #!1 models
> ui mousemode right "tape measure"
> marker segment #13 position 78.15,21.31,38.76 toPosition -51.6,-61.26,-65.26
> color yellow radius 0.1 label 185.7 labelHeight 18.57 labelColor yellow
> marker delete #13
> ui mousemode right "tape measure"
[Repeated 1 time(s)]
> ui mousemode right "pick blobs"
> ui mousemode right "tape measure"
> marker segment #13 position 70.02,38.24,39.59 toPosition
> -86.98,-29.31,-42.67 color yellow radius 0.1 label 189.7 labelHeight 18.97
> labelColor yellow
> ui mousemode right "pick blobs"
> ui mousemode right "translate selected models"
> hide #12 models
> hide #!13 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> open /Users/a13583/Downloads/cryosparc_P121_J1385_002_volume_map_sharp.mrc
Opened cryosparc_P121_J1385_002_volume_map_sharp.mrc as #14, grid size
256,256,256, pixel 1.2, shown at level 0.0852, step 1, values float32
> ui mousemode right select
> volume #14 level 0.5312
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> show #!2 models
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,-170,0,1,0,-5.1531,0,0,1,-87.338
> view matrix models #14,1,0,0,-166.14,0,1,0,-131.21,0,0,1,-154.83
> view matrix models #14,1,0,0,-172.68,0,1,0,-134.74,0,0,1,-153.24
> view matrix models #14,1,0,0,-201.72,0,1,0,-95.007,0,0,1,-233.76
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.83387,0.5473,0.071637,-268.15,-0.53591,0.77169,0.34247,-30.14,0.13215,-0.32397,0.93679,-196.51
> view matrix models
> #14,0.10657,0.91477,-0.38965,-138.62,-0.53881,0.38249,0.75059,-34.498,0.83566,0.12996,0.53366,-311.71
> view matrix models
> #14,-0.79297,-0.37515,0.48007,59.732,0.29911,0.44676,0.84317,-188.83,-0.53079,0.8122,-0.24205,-81.086
> view matrix models
> #14,0.47009,-0.68979,0.55064,-101.17,-0.45502,0.34518,0.82086,-52.798,-0.75629,-0.63643,-0.1516,155.43
> view matrix models
> #14,0.27939,-0.95182,0.12638,32.611,0.36725,0.22755,0.90186,-175.88,-0.88717,-0.20555,0.41314,25.112
> view matrix models
> #14,0.666,-0.7261,0.17094,-68.016,0.55589,0.63592,0.53535,-209.7,-0.49742,-0.26152,0.82715,-90.856
> view matrix models
> #14,0.37947,-0.91097,-0.16168,55.161,0.89222,0.31406,0.32453,-181.93,-0.24486,-0.2674,0.93196,-145.42
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.37947,-0.91097,-0.16168,52.759,0.89222,0.31406,0.32453,-244.96,-0.24486,-0.2674,0.93196,-89.034
> view matrix models
> #14,0.37947,-0.91097,-0.16168,41.755,0.89222,0.31406,0.32453,-245.86,-0.24486,-0.2674,0.93196,-74.798
> view matrix models
> #14,0.37947,-0.91097,-0.16168,41.817,0.89222,0.31406,0.32453,-247.92,-0.24486,-0.2674,0.93196,-71.77
> fitmap #2 inMap #14
Fit molecule fold_ppl_dimer_6his_model_0.cif (#2) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 14164 atoms
average map value = 0.1951, steps = 640
shifted from previous position = 60.1
rotated from previous position = 61.2 degrees
atoms outside contour = 11397, contour level = 0.53118
Position of fold_ppl_dimer_6his_model_0.cif (#2) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.59967909 0.61543074 -0.51149779 171.57886821
-0.11597312 0.69926877 0.70538885 154.09891537
0.79179241 -0.36368695 0.49071028 192.53839785
Axis -0.58180705 -0.70927003 -0.39804093
Axis point -61.74120692 0.00000000 58.72360350
Rotation angle (degrees) 66.74468577
Shift along axis -285.76169972
> transparency sel 50
> view matrix models
> #14,0.37947,-0.91097,-0.16168,33.381,0.89222,0.31406,0.32453,-243.8,-0.24486,-0.2674,0.93196,-66.634
> view matrix models
> #14,0.37947,-0.91097,-0.16168,40.646,0.89222,0.31406,0.32453,-247.36,-0.24486,-0.2674,0.93196,-71.083
> view matrix models
> #14,0.37947,-0.91097,-0.16168,40.033,0.89222,0.31406,0.32453,-249.98,-0.24486,-0.2674,0.93196,-75.381
> fitmap #2 inMap #14
Fit molecule fold_ppl_dimer_6his_model_0.cif (#2) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 14164 atoms
average map value = 0.1951, steps = 80
shifted from previous position = 4.48
rotated from previous position = 0.127 degrees
atoms outside contour = 11399, contour level = 0.53118
Position of fold_ppl_dimer_6his_model_0.cif (#2) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.59842287 0.61694590 -0.51114365 171.53501883
-0.11608631 0.69802473 0.70660134 154.10773077
0.79272570 -0.36350962 0.48933293 192.61050446
Axis -0.58184428 -0.70894416 -0.39856670
Axis point -61.53327777 0.00000000 58.56994293
Rotation angle (degrees) 66.86554015
Shift along axis -285.82857769
> volume #14 level 0.3391
> show #!1 models
> hide #!2 models
> view matrix models
> #14,0.37947,-0.91097,-0.16168,68.692,0.89222,0.31406,0.32453,-212.58,-0.24486,-0.2674,0.93196,-73.446
> view matrix models
> #14,0.37947,-0.91097,-0.16168,69.702,0.89222,0.31406,0.32453,-212.77,-0.24486,-0.2674,0.93196,-72.736
> view matrix models
> #14,0.37947,-0.91097,-0.16168,80.066,0.89222,0.31406,0.32453,-211.97,-0.24486,-0.2674,0.93196,-60.604
> view matrix models
> #14,0.37947,-0.91097,-0.16168,81.568,0.89222,0.31406,0.32453,-210.63,-0.24486,-0.2674,0.93196,-61.709
> view matrix models
> #14,0.37947,-0.91097,-0.16168,92.26,0.89222,0.31406,0.32453,-200.46,-0.24486,-0.2674,0.93196,-68.467
> fitmap #1 inMap #14
Fit molecule fold_ppl_6xhis_model_0.cif (#1) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 7065 atoms
average map value = 0.3216, steps = 536
shifted from previous position = 20.3
rotated from previous position = 40.2 degrees
atoms outside contour = 4042, contour level = 0.33906
Position of fold_ppl_6xhis_model_0.cif (#1) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.76980969 0.33987706 0.54025607 174.33034861
-0.41440044 0.90991570 0.01804700 133.83879565
-0.48545372 -0.23777511 0.84130713 145.90106296
Axis -0.19699267 0.78983517 -0.58082208
Axis point 340.94587609 -0.00000000 -172.53554957
Rotation angle (degrees) 40.49026852
Shift along axis -13.37377121
> lighting flat
> color #1 #d74254ff
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.35744,0.726,-0.5875,-78.66,-0.90543,0.42361,-0.027385,115.13,0.22899,0.54173,0.80876,-241.21
> view matrix models
> #14,-0.25026,0.68804,-0.68115,35.124,-0.95532,-0.061195,0.28918,145.25,0.15728,0.72309,0.67261,-235.8
> view matrix models
> #14,0.059697,0.72954,-0.68133,-18.797,-0.95541,0.23949,0.17273,119.11,0.28918,0.64064,0.71131,-250.03
> fitmap #1 inMap #14
Fit molecule fold_ppl_6xhis_model_0.cif (#1) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 7065 atoms
average map value = 0.4223, steps = 252
shifted from previous position = 1.9
rotated from previous position = 13.2 degrees
atoms outside contour = 3373, contour level = 0.33906
Position of fold_ppl_6xhis_model_0.cif (#1) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
-0.54916204 -0.75624125 -0.35569683 142.44559884
0.29420932 -0.57331690 0.76468857 158.49360234
-0.78221604 0.31528861 0.53733710 137.52857332
Axis -0.36849367 0.34973219 0.86133606
Axis point 77.72789556 88.28797874 0.00000000
Rotation angle (degrees) 142.42642108
Shift along axis 121.39833218
> open
> /Users/a13583/Downloads/fold_ppl_full_length/fold_ppl_full_length_model_0.cif
Chain information for fold_ppl_full_length_model_0.cif #15
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/a13583/Downloads/fold_ppl_full_length/fold_ppl_full_length_model_1.cif
Chain information for fold_ppl_full_length_model_1.cif #16
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/a13583/Downloads/fold_ppl_full_length/fold_ppl_full_length_model_2.cif
Chain information for fold_ppl_full_length_model_2.cif #17
---
Chain | Description
A | .
Computing secondary structure
> open
> /Users/a13583/Downloads/fold_ppl_full_length/fold_ppl_full_length_model_3.cif
Chain information for fold_ppl_full_length_model_3.cif #18
---
Chain | Description
A | .
Computing secondary structure
> hide #15 models
> hide #16 models
> hide #17 models
> hide #!1 models
> view matrix models
> #14,0.19577,0.78915,-0.58217,-63.753,-0.85496,-0.15343,-0.49548,263.63,-0.48032,0.59473,0.64466,-114.24
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.19577,0.78915,-0.58217,-64.822,-0.85496,-0.15343,-0.49548,224.51,-0.48032,0.59473,0.64466,-113
> fitmap #18 inMap #14
Fit molecule fold_ppl_full_length_model_3.cif (#18) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 7005 atoms
average map value = 0.2533, steps = 584
shifted from previous position = 17.9
rotated from previous position = 48.7 degrees
atoms outside contour = 4644, contour level = 0.33906
Position of fold_ppl_full_length_model_3.cif (#18) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
-0.23390748 -0.96384697 0.12761780 143.89240986
0.53333048 -0.01745109 0.84572694 136.71169747
-0.81292428 0.26588432 0.51813091 141.67007070
Axis -0.31161829 0.50546494 0.80461123
Axis point 71.10737879 102.95678196 0.00000000
Rotation angle (degrees) 111.50693427
Shift along axis 138.25279294
> ui mousemode right "rotate selected models"
> view matrix models
> #14,0.61614,0.3351,-0.7128,-43.237,0.11244,0.85829,0.50069,-225.84,0.77957,-0.38864,0.49115,-140.08
> view matrix models
> #14,0.086523,0.52871,-0.84438,30.404,-0.5115,0.75089,0.41776,-101.03,0.85492,0.39575,0.3354,-242.66
> view matrix models
> #14,-0.14306,0.66284,-0.73497,29.443,-0.86036,-0.45035,-0.23869,229.42,-0.48921,0.59819,0.6347,-110.61
> view matrix models
> #14,-0.4068,0.5413,-0.73587,88.109,0.037828,-0.79487,-0.6056,197.42,-0.91273,-0.2742,0.30287,133.43
> view matrix models
> #14,-0.28381,0.18667,-0.94053,152.43,0.77651,0.62021,-0.11122,-199.68,0.56257,-0.7619,-0.32098,72.673
> view matrix models
> #14,-0.27275,-0.30903,-0.9111,218.77,0.30314,0.87117,-0.38624,-121.12,0.91308,-0.38154,-0.14393,-64.309
> view matrix models
> #14,-0.72316,0.062363,-0.68786,199.72,0.62995,-0.34879,-0.69391,54.208,-0.28319,-0.93512,0.21294,146.75
> view matrix models
> #14,-0.45242,-0.14624,-0.87974,217.88,0.8918,-0.079225,-0.44545,-63.814,-0.0045551,-0.98607,0.16626,118.34
> view matrix models
> #14,-0.50725,-0.11199,-0.85449,217.46,0.81312,-0.39071,-0.43148,-8.2033,-0.28554,-0.91367,0.28925,132.27
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.50725,-0.11199,-0.85449,219.31,0.81312,-0.39071,-0.43148,0.81215,-0.28554,-0.91367,0.28925,135.39
> view matrix models
> #14,-0.50725,-0.11199,-0.85449,218.73,0.81312,-0.39071,-0.43148,3.2059,-0.28554,-0.91367,0.28925,134.21
> view matrix models
> #14,-0.50725,-0.11199,-0.85449,217.77,0.81312,-0.39071,-0.43148,5.5612,-0.28554,-0.91367,0.28925,133.81
> view matrix models
> #14,-0.50725,-0.11199,-0.85449,219.53,0.81312,-0.39071,-0.43148,4.0293,-0.28554,-0.91367,0.28925,131.45
> view matrix models
> #14,-0.50725,-0.11199,-0.85449,221.42,0.81312,-0.39071,-0.43148,1.109,-0.28554,-0.91367,0.28925,137.11
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.45998,-0.087913,-0.88357,215.05,0.88572,-0.11564,-0.44959,-47.596,-0.062651,-0.98939,0.13106,138.04
> view matrix models
> #14,-0.44097,-0.062475,-0.89534,210.2,0.89461,0.049693,-0.44408,-74.02,0.072236,-0.99681,0.033977,133.19
> open
> /Users/a13583/Downloads/fold_ppl_full_length/fold_ppl_full_length_model_4.cif
Chain information for fold_ppl_full_length_model_4.cif #19
---
Chain | Description
A | .
Computing secondary structure
> hide #18 models
> fitmap #19 inMap #14
Fit molecule fold_ppl_full_length_model_4.cif (#19) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 7005 atoms
average map value = 0.2991, steps = 408
shifted from previous position = 27.6
rotated from previous position = 65.9 degrees
atoms outside contour = 4192, contour level = 0.33906
Position of fold_ppl_full_length_model_4.cif (#19) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.34726593 0.59212226 0.72718471 159.75228111
0.11421617 0.74296388 -0.65951447 152.01630221
-0.93078517 0.31208316 0.19037611 176.13766486
Axis 0.49065204 0.83726666 -0.24134023
Axis point 183.55746504 0.00000000 55.16166991
Rotation angle (degrees) 81.93462227
Shift along axis 163.15186038
> view matrix models
> #14,-0.64858,0.41436,0.63847,-62.851,-0.27819,0.65175,-0.70557,59.096,-0.70848,-0.63524,-0.30745,253.22
> view matrix models
> #14,0.29462,-0.40177,-0.86705,141.92,0.058531,0.91321,-0.40327,-77.564,0.95382,0.068063,0.29256,-198.54
> fitmap #19 inMap #14
Fit molecule fold_ppl_full_length_model_4.cif (#19) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 7005 atoms
average map value = 0.3041, steps = 228
shifted from previous position = 21.7
rotated from previous position = 31 degrees
atoms outside contour = 4152, contour level = 0.33906
Position of fold_ppl_full_length_model_4.cif (#19) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
0.07488014 -0.39312296 0.91643183 162.14415428
0.29290662 0.88714345 0.35662616 161.20235217
-0.95320443 0.24172473 0.18157774 178.28907015
Axis -0.05759938 0.93723714 0.34390240
Axis point 148.20003600 0.00000000 -40.08749476
Rotation angle (degrees) 85.88258222
Shift along axis 203.05946751
> view matrix models
> #14,0.3612,-0.34793,-0.86515,123.46,0.0081453,0.92893,-0.37018,-77.161,0.93245,0.12666,0.33836,-210.84
> ui mousemode right "translate selected models"
> view matrix models
> #14,0.3612,-0.34793,-0.86515,110.34,0.0081453,0.92893,-0.37018,-77.388,0.93245,0.12666,0.33836,-199.66
> view matrix models
> #14,0.3612,-0.34793,-0.86515,102.7,0.0081453,0.92893,-0.37018,-78.467,0.93245,0.12666,0.33836,-190.68
> view matrix models
> #14,0.3612,-0.34793,-0.86515,105.01,0.0081453,0.92893,-0.37018,-82.275,0.93245,0.12666,0.33836,-191.88
> volume #14 level 0.3179
> volume #14 level 0.3744
> view matrix models
> #14,0.3612,-0.34793,-0.86515,104.76,0.0081453,0.92893,-0.37018,-83.146,0.93245,0.12666,0.33836,-192.19
> fitmap #19 inMap #14
Fit molecule fold_ppl_full_length_model_4.cif (#19) to map
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) using 7005 atoms
average map value = 0.4163, steps = 820
shifted from previous position = 10.7
rotated from previous position = 108 degrees
atoms outside contour = 3468, contour level = 0.37438
Position of fold_ppl_full_length_model_4.cif (#19) relative to
cryosparc_P121_J1385_002_volume_map_sharp.mrc (#14) coordinates:
Matrix rotation and translation
-0.75700053 -0.53062504 -0.38129682 144.89261712
0.21592044 -0.75390620 0.62048675 153.20231318
-0.61670785 0.38737902 0.68528018 145.53935303
Axis -0.28540738 0.28822744 0.91403915
Axis point 81.84878928 75.10351907 0.00000000
Rotation angle (degrees) 155.89706684
Shift along axis 135.83235453
> close #15
> close #16
> close #17
> close #18
> show #!1 models
> open /Users/a13583/Desktop/PPL/AF3/fold_ppl_6xhis/fold_ppl_6xhis_model_1.cif
Chain information for fold_ppl_6xhis_model_1.cif #15
---
Chain | Description
A | .
Computing secondary structure
> open /Users/a13583/Desktop/PPL/AF3/fold_ppl_6xhis/fold_ppl_6xhis_model_2.cif
Chain information for fold_ppl_6xhis_model_2.cif #16
---
Chain | Description
A | .
Computing secondary structure
> open /Users/a13583/Desktop/PPL/AF3/fold_ppl_6xhis/fold_ppl_6xhis_model_3.cif
Chain information for fold_ppl_6xhis_model_3.cif #17
---
Chain | Description
A | .
Computing secondary structure
> open /Users/a13583/Desktop/PPL/AF3/fold_ppl_6xhis/fold_ppl_6xhis_model_4.cif
Chain information for fold_ppl_6xhis_model_4.cif #18
---
Chain | Description
A | .
Computing secondary structure
> close #18
> close #17
> close #16
> close #15
> hide #!1 models
Traceback (most recent call last):
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> hide #!14 models
> hide #19 models
> select subtract #14
Nothing selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1409_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 825, in update_drawings
levels, colors = self.initial_surface_levels()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 626, in initial_surface_levels
mstats = self.matrix_value_statistics()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1759, in matrix_value_statistics
matrices = self.displayed_matrices(read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1794, in displayed_matrices
matrices.append(self.matrix(read_matrix))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1277, in matrix
m = self.region_matrix(r, read_matrix)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1301, in region_matrix
m = d.matrix(origin, size, step, progress, from_cache_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/griddata.py", line 317, in matrix
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_grid.py", line 50, in read_matrix
m = self.mrc_data.read_matrix(ijk_origin, ijk_size, ijk_step, progress)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/mrc/mrc_format.py", line 287, in read_matrix
matrix = read_array(self.path, self.data_offset,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 61, in read_array
progress.plane((k-ko)//kstep)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/progress.py", line 114, in plane
self.show_status(self.format % pct)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/progress.py", line 80, in show_status
self.message(text)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_data/progress.py", line 57, in message
log.status(text)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1409_002_volume_map_sharp.mrc
Opened cryosparc_P121_J1409_002_volume_map_sharp.mrc as #15, grid size
384,384,384, pixel 1.2, shown at level 0.104, step 2, values float32
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 326, in provider_open
session.logger.status(status, log=status)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> rename #15 cryosparc_P121_J1409_002_volume_map_sharp.mrc-四聚体
> view
> volume #15 level 0.2752
> transparency #15.1 50
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1393, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 971, in
toggle_surface_transparency
run_on_models('transparency %%s %d' % trans, model_class = Surface)(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 594, in run_expanded_command
run(session, cmd)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/transparency.py", line 105, in transparency
session.logger.status('Set transparency of %s' % commas(what, 'and'))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open "/Users/a13583/Desktop/PPL/AF3/fold_ppl_tetramer
> (1)/fold_ppl_tetramer_model_0.cif"
Chain information for fold_ppl_tetramer_model_0.cif #16
---
Chain | Description
A B C D | .
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 326, in provider_open
session.logger.status(status, log=status)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
Computing secondary structure
> select add #16
28020 atoms, 28608 bonds, 3564 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> hide #16 models
> show #16 models
> select subtract #16
Nothing selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> select add #16
28020 atoms, 28608 bonds, 3564 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> view matrix models #16,1,0,0,-13.426,0,1,0,198.84,0,0,1,185.95
> view matrix models #16,1,0,0,159.82,0,1,0,262.11,0,0,1,239.48
> view matrix models #16,1,0,0,164.58,0,1,0,263.05,0,0,1,243.29
> view matrix models #16,1,0,0,190.69,0,1,0,234.49,0,0,1,199.94
> view matrix models #16,1,0,0,212.23,0,1,0,228.1,0,0,1,202.75
> view matrix models #16,1,0,0,212.31,0,1,0,227.82,0,0,1,213.97
> fitmap #16 inMap #15
Fit molecule fold_ppl_tetramer_model_0.cif (#16) to map
cryosparc_P121_J1409_002_volume_map_sharp.mrc-四聚体 (#15) using 28020 atoms
average map value = 0.1054, steps = 260
shifted from previous position = 14.8
rotated from previous position = 34.1 degrees
atoms outside contour = 21710, contour level = 0.27518
Position of fold_ppl_tetramer_model_0.cif (#16) relative to
cryosparc_P121_J1409_002_volume_map_sharp.mrc-四聚体 (#15) coordinates:
Matrix rotation and translation
0.82910844 0.40472585 -0.38571515 225.81617054
-0.38347212 0.91371213 0.13445920 221.35984501
0.40685172 0.03642975 0.91276752 211.60660720
Axis -0.08736528 -0.70634717 -0.70245355
Axis point 137.27165484 -0.00000000 451.07781935
Rotation angle (degrees) 34.12720414
Shift along axis -324.72920397
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1393, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 832, in fit_in_map
run(session, 'fit #%s in #%s' % (model.id_string, map.id_string))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 138, in fitmap
fits = [fit_atoms_in_map(atoms, volume, shift, rotate, mwm,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 298, in fit_atoms_in_map
log.status('%d steps, shift %.3g, rotation %.3g degrees, average map value
%.4g'
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> view matrix models
> #16,0.82911,0.40473,-0.38572,221.81,-0.38347,0.91371,0.13446,214.93,0.40685,0.03643,0.91277,225.76
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.98034,-0.18143,-0.077593,224.53,0.19725,0.91204,0.35956,222.74,0.0055347,-0.36779,0.92989,220.83
> view matrix models
> #16,0.85792,-0.48014,0.18284,224.11,0.50945,0.7489,-0.4238,222.43,0.066555,0.45674,0.88711,222.06
> view matrix models
> #16,0.71417,-0.61733,0.32994,223.03,0.69773,0.66553,-0.26504,225.3,-0.055963,0.41949,0.90603,220.7
> view matrix models
> #16,0.49374,-0.65286,0.57445,221.63,0.80911,0.58697,-0.028348,227.67,-0.31868,0.47879,0.81805,217.28
> view matrix models
> #16,0.3461,-0.72934,0.59015,219.92,0.85394,0.50542,0.12382,228.85,-0.38859,0.4611,0.79774,216.36
> view matrix models
> #16,0.26848,-0.77082,0.57772,218.92,0.88728,0.43138,0.16322,229.36,-0.37503,0.46878,0.79975,216.53
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.26848,-0.77082,0.57772,229.51,0.88728,0.43138,0.16322,233.26,-0.37503,0.46878,0.79975,221.83
> view matrix models
> #16,0.26848,-0.77082,0.57772,235.25,0.88728,0.43138,0.16322,225.08,-0.37503,0.46878,0.79975,223.29
> view matrix models
> #16,0.26848,-0.77082,0.57772,234.59,0.88728,0.43138,0.16322,222.99,-0.37503,0.46878,0.79975,226.03
> view matrix models
> #16,0.26848,-0.77082,0.57772,233.93,0.88728,0.43138,0.16322,227.51,-0.37503,0.46878,0.79975,227.17
> ui mousemode right "rotate selected models"
> view matrix models
> #16,0.81404,0.0084976,0.58074,240.96,0.21821,0.92216,-0.31937,217.86,-0.53825,0.38671,0.74883,224.96
> ui mousemode right "translate selected models"
> view matrix models
> #16,0.81404,0.0084976,0.58074,241.96,0.21821,0.92216,-0.31937,212.24,-0.53825,0.38671,0.74883,226.18
> open "/Users/a13583/Desktop/PPL/AF3/fold_ppl_tetramer
> (1)/fold_ppl_tetramer_model_1.cif"
Chain information for fold_ppl_tetramer_model_1.cif #17
---
Chain | Description
A B C D | .
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 326, in provider_open
session.logger.status(status, log=status)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
Computing secondary structure
> close #17
> open "/Users/a13583/Desktop/PPL/AF3/fold_ppl_tetramer
> (1)/fold_ppl_tetramer_model_2.cif"
Chain information for fold_ppl_tetramer_model_2.cif #17
---
Chain | Description
A B C D | .
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 326, in provider_open
session.logger.status(status, log=status)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
Computing secondary structure
> open "/Users/a13583/Desktop/PPL/AF3/fold_ppl_tetramer
> (1)/fold_ppl_tetramer_model_3.cif"
Chain information for fold_ppl_tetramer_model_3.cif #18
---
Chain | Description
A B C D | .
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 326, in provider_open
session.logger.status(status, log=status)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
Computing secondary structure
> hide #17 models
> open "/Users/a13583/Desktop/PPL/AF3/fold_ppl_tetramer
> (1)/fold_ppl_tetramer_model_4.cif"
Chain information for fold_ppl_tetramer_model_4.cif #20
---
Chain | Description
A B C D | .
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 326, in provider_open
session.logger.status(status, log=status)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
Computing secondary structure
> hide #18 models
> hide #16 models
> select subtract #16
Nothing selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> select add #20
28020 atoms, 28608 bonds, 3564 residues, 1 model selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 120, in select_add
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> view matrix models #20,1,0,0,9.5521,0,1,0,6.77,0,0,1,45.281
> view matrix models #20,1,0,0,2.7605,0,1,0,6.5467,0,0,1,32.101
> view matrix models #20,1,0,0,122.53,0,1,0,4.7446,0,0,1,240.75
> view matrix models #20,1,0,0,209.4,0,1,0,175.94,0,0,1,151.84
> view matrix models #20,1,0,0,195.33,0,1,0,180.2,0,0,1,189.37
> view matrix models #20,1,0,0,198.12,0,1,0,181.61,0,0,1,192.72
> view matrix models #20,1,0,0,201.97,0,1,0,212.07,0,0,1,219.81
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.64853,0.73327,-0.20426,196.76,-0.71101,0.67938,0.1814,205.25,0.27178,0.027589,0.96196,222.62
> view matrix models
> #20,0.37983,0.86116,-0.33783,193.08,-0.83551,0.47612,0.2743,204.41,0.39706,0.17808,0.90035,223.63
> view matrix models
> #20,-0.10405,-0.85378,0.51013,192.65,0.60411,0.3532,0.71435,222.53,-0.79008,0.38251,0.47902,208.37
> ui mousemode right "translate selected models"
> view matrix models
> #20,-0.10405,-0.85378,0.51013,217.34,0.60411,0.3532,0.71435,229.93,-0.79008,0.38251,0.47902,208.68
> view matrix models
> #20,-0.10405,-0.85378,0.51013,218.48,0.60411,0.3532,0.71435,228.24,-0.79008,0.38251,0.47902,217.94
> view matrix models
> #20,-0.10405,-0.85378,0.51013,212.46,0.60411,0.3532,0.71435,227.28,-0.79008,0.38251,0.47902,225.73
> ui mousemode right "rotate selected models"
> view matrix models
> #20,0.908,0.41887,0.0095428,220.63,-0.40603,0.88533,-0.22657,211.28,-0.10335,0.20185,0.97395,235.81
> view matrix models
> #20,0.80574,0.57005,-0.16069,218.6,-0.59211,0.76913,-0.24049,209.21,-0.013501,0.28892,0.95726,236.69
> view matrix models
> #20,0.74913,0.61907,-0.2357,217.58,-0.66124,0.72011,-0.21024,208.61,0.039576,0.31335,0.94881,237.22
> ui mousemode right "translate selected models"
> view matrix models
> #20,0.74913,0.61907,-0.2357,210.35,-0.66124,0.72011,-0.21024,228.58,0.039576,0.31335,0.94881,229.55
> view matrix models
> #20,0.74913,0.61907,-0.2357,221.82,-0.66124,0.72011,-0.21024,229.12,0.039576,0.31335,0.94881,222.15
> fitmap #20 inMap #15
Fit molecule fold_ppl_tetramer_model_4.cif (#20) to map
cryosparc_P121_J1409_002_volume_map_sharp.mrc-四聚体 (#15) using 28020 atoms
average map value = 0.1669, steps = 152
shifted from previous position = 17.2
rotated from previous position = 12 degrees
atoms outside contour = 19964, contour level = 0.27518
Position of fold_ppl_tetramer_model_4.cif (#20) relative to
cryosparc_P121_J1409_002_volume_map_sharp.mrc-四聚体 (#15) coordinates:
Matrix rotation and translation
0.59869431 0.76015013 -0.25246168 238.36913778
-0.80097741 0.56839407 -0.18805149 231.76690665
0.00055036 0.31480146 0.94915738 225.41414734
Axis 0.30301170 -0.15246129 -0.94071221
Axis point 360.15612662 -193.26571782 0.00000000
Rotation angle (degrees) 56.07391820
Shift along axis -175.15668444
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 230, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/__init__.py", line 66, in run_provider
shortcuts.run_provider(session, name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 1393, in run_provider
keyboard_shortcuts(session).try_shortcut(name)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 403, in try_shortcut
self.run_shortcut(keys)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 421, in run_shortcut
sc.run(self.session, status = self._enabled)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 340, in run
f(s)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 832, in fit_in_map
run(session, 'fit #%s in #%s' % (model.id_string, map.id_string))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/shortcuts/shortcuts.py", line 537, in run
run_command(session, command, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 138, in fitmap
fits = [fit_atoms_in_map(atoms, volume, shift, rotate, mwm,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map_fit/fitcmd.py", line 298, in fit_atoms_in_map
log.status('%d steps, shift %.3g, rotation %.3g degrees, average map value
%.4g'
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> hide #20 models
> show #20 models
> select subtract #20
Nothing selected
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 480, in _tree_change_cb
run(self.session, "select " + mode + " #" + model.id_string)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 132, in select_subtract
report_selection(session)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/std_commands/select.py", line 192, in report_selection
session.logger.status(', '.join(lines) + ' selected', log = True)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> volume #15 level 0.2575
> volume #15 level 0.2279
Traceback (most recent call last):
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> hide #20 models
> hide #!15 models
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> close #13
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Failed opening file
/Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc:
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Failed opening file
/Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc:
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Failed opening file
/Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc:
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Failed opening file
/Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc:
GLError(
err = 1286,
description = b'invalid framebuffer operation',
baseOperation = glClear,
cArguments = (16640,)
)
> close #14
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1398_004_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> show #!1 models
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/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.
> open /Users/a13583/Downloads/cryosparc_P121_J1415_002_volume_map_sharp.mrc
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 54, in event
if self.handle_drag_and_drop(event):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/graphics.py", line 124, in handle_drag_and_drop
mw.dropEvent(event)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 816, in dropEvent
_open_dropped_file(self.session, p)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 2202, in _open_dropped_file
run(session, 'open %s' % FileNameArg.unparse(path))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 194, in provider_open
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 527, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 498, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 183, in open
return open_map(session, path, format=_name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3752, in open_map
smodels, smsg = open_grids(session, sgrids, name, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3854, in open_grids
v.update_drawings()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 830, in update_drawings
self._update_surfaces()
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 853, in _update_surfaces
s.update_surface(ro)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 2212, in update_surface
v.message('Computing %s surface, level %.3g' % (v.data.name, level))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/map/volume.py", line 122, in message
self.message_cb(text, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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
"/Applications/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
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2808, in res_hover
_residue_mouse_hover(pick, session.logger)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2801, in _residue_mouse_hover
log.status("chain %s: %s" % (chain.chain_id, chain.description))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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,)
)
Traceback (most recent call last):
File
"/Applications/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
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2808, in res_hover
_residue_mouse_hover(pick, session.logger)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 2801, in _residue_mouse_hover
log.status("chain %s: %s" % (chain.chain_id, chain.description))
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 522, in status
StatusLogger.status(self, msg, **kw)
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/logger.py", line 220, in status
if l.status(msg, color, secondary) and getattr(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 1133, in status
sbar.status(msg, color, secondary)
File
"/Applications/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
"/Applications/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,)
)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File
"/Applications/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
"/Applications/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
"/Applications/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.
Error processing trigger "mouse hover":
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.
OpenGL version: 4.1 Metal - 90.5
OpenGL renderer: Apple M4
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: Mac mini
Model Identifier: Mac16,10
Model Number: MU9D3CH/A
Chip: Apple M4
Total Number of Cores: 10 (4 Performance and 6 Efficiency)
Memory: 16 GB
System Firmware Version: 13822.81.10
OS Loader Version: 13822.81.10
Software:
System Software Overview:
System Version: macOS 26.3 (25D125)
Kernel Version: Darwin 25.3.0
Time since boot: 32天18小时52分钟
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
Type: GPU
Bus: Built-In
Total Number of Cores: 10
Vendor: Apple (0x106b)
Metal Support: Metal 4
Displays:
Mi Monitor:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 180.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
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-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-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.3
ChimeraX-Label: 1.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.12
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.13.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.19
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.61.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.1
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine-commercial: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.2
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.21
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
roman-numerals-py: 4.1.0
rpds-py: 0.30.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.2.0
stack-data: 0.6.3
starlette: 0.52.1
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.4
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
urllib3: 2.6.3
uvicorn: 0.40.0
wcwidth: 0.3.2
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
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