id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17810 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.3-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x00000002a145f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a0453000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029f447000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029e43b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029d42f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029c423000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029b417000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029a40b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002993ff000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002983f3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002973e7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001e2699c40 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/leela/Downloads/fold_vgrgtox_immunity3_with_mg/fold_vgrgtox_immunity3_with_mg_model_0.cif Chain information for fold_vgrgtox_immunity3_with_mg_model_0.cif #1 --- Chain | Description A B C | . D E F | . > hide cartoons > show cartoons Computing secondary structure > style sphere Changed 25881 atom styles > hide atoms > select /A:1-918 7062 atoms, 7177 bonds, 918 residues, 1 model selected > sequence chain #1/A#1/B#1/C Alignment identifier is 1 > select /A-C:1-2 45 atoms, 42 bonds, 6 residues, 1 model selected > select /A-C:1-495 11577 atoms, 11796 bonds, 1485 residues, 1 model selected > select add #1 25881 atoms, 26313 bonds, 3342 residues, 1 model selected > select subtract #1 Nothing selected > ui mousemode right select > select /B:482 5 atoms, 4 bonds, 1 residue, 1 model selected > select /B:481 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:482 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select /B:482 5 atoms, 4 bonds, 1 residue, 1 model selected > select /C:483 7 atoms, 7 bonds, 1 residue, 1 model selected > select /B:483 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /A:486 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /A:487 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:508 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:507 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:508 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:486 7 atoms, 6 bonds, 1 residue, 1 model selected Drag select of 2 residues > select /C:707 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A-C:707 27 atoms, 24 bonds, 3 residues, 1 model selected > select /A-C:707-918 4929 atoms, 4998 bonds, 636 residues, 1 model selected > select > /A-C:9-11,46-48,50-55,102-106,122-132,159-170,209-216,225-228,275-277,286-288,356-358,373-376,508-544,547-556,558-577,582-622,625-683,707-716,751-753,784-799,827-829,849-864,900-916 6888 atoms, 6903 bonds, 891 residues, 1 model selected > select /C:707 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A-C:707 27 atoms, 24 bonds, 3 residues, 1 model selected > select /A-C:1-707 16284 atoms, 16557 bonds, 2121 residues, 1 model selected > hide sel cartoons > hide #1 models > show #1 models > select add #1 25881 atoms, 26313 bonds, 3342 residues, 1 model selected > select subtract #1 Nothing selected > select /A-C:1-2 45 atoms, 42 bonds, 6 residues, 1 model selected > select /A-C:918 30 atoms, 27 bonds, 3 residues, 1 model selected > select /A-C:871-918 1125 atoms, 1131 bonds, 144 residues, 1 model selected > select /A-C:870-871 48 atoms, 45 bonds, 6 residues, 1 model selected > select /A-C:91-871 17955 atoms, 18261 bonds, 2343 residues, 1 model selected > select > /A-C:9-11,46-48,50-55,102-106,122-132,159-170,209-216,225-228,275-277,286-288,356-358,373-376,508-544,547-556,558-577,582-622,625-683,707-716,751-753,784-799,827-829,849-864,900-916 6888 atoms, 6903 bonds, 891 residues, 1 model selected > select /A-C:46 27 atoms, 24 bonds, 3 residues, 1 model selected > select /A-C:46-918 20103 atoms, 20430 bonds, 2619 residues, 1 model selected > show sel cartoons > ui mousemode right select > select /A-C:918 30 atoms, 27 bonds, 3 residues, 1 model selected > select /A-C 21186 atoms, 21531 bonds, 2754 residues, 1 model selected > select /A-C:918 30 atoms, 27 bonds, 3 residues, 1 model selected > select /A-C:917-918 48 atoms, 45 bonds, 6 residues, 1 model selected > select /A:508 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A-C:917-918 48 atoms, 45 bonds, 6 residues, 1 model selected > select /A:918 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:918 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:918 10 atoms, 9 bonds, 1 residue, 1 model selected > select /C:508 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C:683 9 atoms, 8 bonds, 1 residue, 1 model selected > select /C:508 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:681 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select /A:684 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:299 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:683 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:684 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /A:684 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /A:750 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select /A:750 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:751 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:918 10 atoms, 9 bonds, 1 residue, 1 model selected > select /A:752 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:751 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:918 10 atoms, 9 bonds, 1 residue, 1 model selected > color #1 #9e56e5ff > undo > select /A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A-C 21186 atoms, 21531 bonds, 2754 residues, 1 model selected > color #1 #feffa3ff > select /C:1-918 7062 atoms, 7177 bonds, 918 residues, 1 model selected > select /F:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /F:175 6 atoms, 5 bonds, 1 residue, 1 model selected > select /F:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /E:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > color white sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white sel cartoons Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white sel atoms Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white sel models Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > rainbow sel > white sel Unknown command: white sel > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface"": minimum -27.46, mean -5.478, maximum 23.9 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > color white > color palegreen yellow Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 #fafba0ff > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_D SES surface #1.1: minimum, -22.01, mean -7.61, maximum 4.10 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > color select Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color select random Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color white select Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white All select Expected ',' or a keyword > color white all, select Missing or invalid ""what"" argument: Should be one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' > color white All aroms select Expected ',' or a keyword > color white All atoms select Expected ',' or a keyword > color white atoms > color white ribbons > select /F:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /C:1-918 7062 atoms, 7177 bonds, 918 residues, 1 model selected > select /F:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /E:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /E:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > sequence chain #1/D#1/E#1/F Alignment identifier is 2 > select /D-F:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /D-F 4692 atoms, 4782 bonds, 585 residues, 1 model selected > color white ribbons > color #1.1 #ed7fe5ff > show sel cartoons > hide sel atoms > hide sel cartoons > color #1 #feffa3ff > show sel cartoons > log metadata #1 No models had metadata > log chains #1 Chain information for fold_vgrgtox_immunity3_with_mg_model_0.cif #1 --- Chain | Description A B C | . D E F | . > select /E:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /F:1-195 1564 atoms, 1594 bonds, 195 residues, 1 model selected > select /D-F:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select /D-F 4692 atoms, 4782 bonds, 585 residues, 1 model selected > color #1 #63633fff > color #1 #8c8d59ff > color #1 #feffa1ff > Color DEF chains Unknown command: Color DEF chains > color red #1/D Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red :D Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red ribbons :D Expected ',' or a keyword > color red /D & ribbons Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white ribbons :D,E,F Expected ',' or a keyword > color white /DEF Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color white All /DEF Expected ',' or a keyword > ui tool show ""Color Actions"" > color sel white > show Mg > select clear > color mg Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword Drag select of 4 residues > select /G:1@MG 1 atom, 1 residue, 1 model selected > color sel red > select sel @ select sel @ select sel @ undo > select /A:873 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:874 11 atoms, 11 bonds, 1 residue, 1 model selected > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ ui tool show ""Side View"" > lighting shadows false > graphics silhouettes true > graphics silhouettes false > lighting shadows true > lighting shadows false > lighting flat > lighting full > lighting flat > lighting full > lighting flat > lighting full > lighting flat > lighting soft > lighting simple > lighting soft > lighting full > lighting flat > view orient > view > view sel > ui tool show ""Side View"" > view sel > view > lighting full > set bgColor white > set bgColor gray > set bgColor black Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 0 maps. > transparency 50 > volume hide No volumes specified > volume hide No volumes specified > volume hide No volumes specified > save /Users/leela/Desktop/image1.png supersample 3 > set bgColor white > set bgColor black > view orient > set bgColor white > save /Users/leela/Desktop/image2.png supersample 3 > select clear > select /H:1@MG 1 atom, 1 residue, 1 model selected > color sel red > select /I:1@MG 1 atom, 1 residue, 1 model selected > color sel red > save /Users/leela/Desktop/image3.png supersample 3 > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ show sel atoms > hide sel atoms > show sel atoms > style sel stick Changed 18 atom styles > hide sel atoms > show sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > style sel stick Changed 18 atom styles > style sel stick Changed 18 atom styles > style sel sphere Changed 18 atom styles > style sel stick Changed 18 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > style sel ball Changed 18 atom styles > style sel ball Changed 18 atom styles > style sel stick Changed 18 atom styles > hide sel surfaces > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > select /A:828 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > volume hide No volumes specified > volume style surface No volumes specified > volume style mesh No volumes specified > volume style mesh No volumes specified > volume style image No volumes specified > transparency 0 > volume showOutlineBox true No volumes specified > hide sel surfaces > hide sel cartoons > show sel cartoons > hide sel atoms > select /A:873@CG 1 atom, 1 residue, 1 model selected > select /A:873@CB 1 atom, 1 residue, 1 model selected > select /A:873 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:873 9 atoms, 8 bonds, 1 residue, 1 model selected > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface #1.2: minimum, -24.71, mean -2.57, maximum 15.92 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface #1.2: minimum, -24.71, mean -2.57, maximum 15.92 To also show corresponding color key, enter the above coulombic command and add key true > undo > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface #1.2: minimum, -24.71, mean -2.57, maximum 15.92 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface #1.2: minimum, -24.71, mean -2.57, maximum 15.92 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface #1.2: minimum, -24.71, mean -2.57, maximum 15.92 To also show corresponding color key, enter the above coulombic command and add key true > undo > select /A:873@NE2 1 atom, 1 residue, 1 model selected > hide sel surfaces > select /A:873@OE1 1 atom, 1 residue, 1 model selected > hide sel surfaces > select /A:873@CB 1 atom, 1 residue, 1 model selected > hide sel surfaces > select clear > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ select /A:873@N 1 atom, 1 residue, 1 model selected > hide sel surfaces > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ select /A:873 9 atoms, 8 bonds, 1 residue, 1 model selected > hide sel surfaces > hide sel atoms > show sel atoms > hide sel surfaces > style sel sphere Changed 9 atom styles > style sel stick Changed 9 atom styles > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel surfaces > show sel surfaces > show sel atoms > hide sel atoms > select /A:871 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:871 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel cartoons > show sel cartoons > hide sel surfaces > style sel stick Changed 8 atom styles > select clear > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ select /A:828 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel stick Changed 9 atom styles > style sel stick Changed 9 atom styles > style sel stick Changed 9 atom styles > show sel atoms Drag select of 32 residues > select clear > save /Users/leela/Desktop/image4.png supersample 3 > select clear > select /G:1@MG 1 atom, 1 residue, 1 model selected > select sel @ label residues > save /Users/leela/Desktop/image5.png supersample 3 > label (#!1 & sel) attribute name > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > save /Users/leela/Desktop/image6.png supersample 3 > save /Users/leela/Desktop/image7.png supersample 3 > coulombic sel Coulombic values for fold_vgrgtox_immunity3_with_mg_model_0.cif_A SES surface #1.2: minimum, -24.71, mean -2.57, maximum 15.92 To also show corresponding color key, enter the above coulombic command and add key true > select clear > save /Users/leela/Desktop/image8.png supersample 3 > save /Users/leela/Desktop/image9.png supersample 3 > select /A:622 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show Distances > select clear > select /B:69 8 atoms, 7 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select /A:622 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select /B:69 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /A:622 17 atoms, 15 bonds, 2 residues, 1 model selected > select /A:622 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:69 8 atoms, 7 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select /A:622 9 atoms, 8 bonds, 1 residue, 1 model selected > style sel sphere Changed 9 atom styles > show sel atoms > select /A:622@OE1 1 atom, 1 residue, 1 model selected > select /A:622@OE1 1 atom, 1 residue, 1 model selected > select clear > select /B:69 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel sphere Changed 8 atom styles > style sel sphere Changed 8 atom styles > show sel atoms > select /B:69@CB 1 atom, 1 residue, 1 model selected > select add /A:622@OE1 2 atoms, 2 residues, 1 model selected > select /A:622@CA 1 atom, 1 residue, 1 model selected > select add /B:69@ND2 2 atoms, 2 residues, 2 models selected > distance /A:622@CA /B:69@ND2 Distance between /A GLU 622 CA and /B ASN 69 ND2: 172.230Å ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,13 Model Number: MRYN3ZP/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3 (23D2057) Kernel Version: Darwin 23.3.0 Time since boot: 27 days, 20 hours, 59 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2880 x 1864 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL P2419H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX