id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15286 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.3.1-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003123de000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000201018240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 1014 in to_h36 File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 1084 in _h_name File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 949 in new_hydrogen File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 910 in add_altloc_hyds File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 909 in _attach_hydrogens File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/hbond.py"", line 764 in add_hydrogens File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 184 in hbond_add_hydrogens File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/cmd.py"", line 77 in cmd_addh File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py"", line 95 in assign_charges File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py"", line 99 in cmd_coulombic File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 525 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 582 in run_expanded_command File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 72 in func_plus_tip File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 339 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 420 in run_shortcut File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 402 in try_shortcut File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1376 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py"", line 66 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1302 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 397 in run_provider File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py"", line 205 in callback File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, lxml._elementpath, lxml.etree, chimerax.map._map, openmm._openmm, openmm.app.internal.compiled, 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crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb"" Chain information for B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb #1 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb"" Chain information for B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb #2 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb"" Chain information for B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb #3 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb"" Chain information for B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb #4 --- Chain | Description A | No description available > select clear > mmaker #2,3,4 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 B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb, chain A (#1) with B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb, chain A (#2), sequence alignment score = 845.9 RMSD between 67 pruned atom pairs is 1.241 angstroms; (across all 216 pairs: 12.206) Matchmaker B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb, chain A (#1) with B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb, chain A (#3), sequence alignment score = 409.1 RMSD between 60 pruned atom pairs is 0.983 angstroms; (across all 199 pairs: 24.402) Matchmaker B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb, chain A (#1) with B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb, chain A (#4), sequence alignment score = 387.3 RMSD between 85 pruned atom pairs is 1.144 angstroms; (across all 195 pairs: 41.074) > select clear > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain Drag select of 166 residues > hide sel cartoons Drag select of 44 residues > hide sel cartoons Drag select of 150 residues > hide sel cartoons Drag select of 19 residues > hide sel cartoons Drag select of 26 residues > hide sel cartoons Drag select of 1 residues > hide sel cartoons Drag select of 39 residues > hide sel cartoons > select clear Drag select of 432 residues > show sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb_A SES surface #1.1: minimum, -24.37, mean -3.30, maximum 13.45 Coulombic values for B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb_A SES surface #2.1: minimum, -20.31, mean -1.50, maximum 16.74 Coulombic values for B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb_A SES surface #3.1: minimum, -23.13, mean -2.88, maximum 14.21 Coulombic values for B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb_A SES surface #4.1: minimum, -17.29, mean -1.27, maximum 16.16 To also show corresponding color key, enter the above coulombic command and add key true > tile 4 models tiled > select clear > preset custom pretty-chain Using preset: Custom / Pretty-chain Preset expands to these ChimeraX commands: lighting soft set bgColor white cartoon style coil width 1.5 thickness 0.8 cartoon style helix xsection round width 3 thickness 0.8 cartoon style strand xsection round width 3 thickness 0.8 cartoon style strand arrowscale 1 cartoon style helix xsection oval sides 10 graphics silhouettes true graphics silhouettes width 1.5 graphics silhouettes depthJump 0.003 lighting msDepthBias 0.004 lighting shadows true intensity 0.06 lighting depthCueColor #000000 color bychain Drag select of B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb_A SES surface, 129886 of 311652 triangles, B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb_A SES surface, 128941 of 330650 triangles, B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb_A SES surface, 141145 of 302144 triangles, B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb_A SES surface, 141317 of 288802 triangles, 432 residues > coulombic sel Coulombic values for B_Human_CHM4B_Q9H444_85b26_unrelaxed_rank_1_model_4.pdb_A SES surface #1.1: minimum, -24.37, mean -3.30, maximum 13.45 Coulombic values for B_Human_CHM4C_Q96CF2_2ce07_unrelaxed_rank_1_model_4.pdb_A SES surface #2.1: minimum, -20.31, mean -1.50, maximum 16.74 Coulombic values for B_Human_CHMP5_Q9NZZ3_56a78_unrelaxed_rank_1_model_4.pdb_A SES surface #3.1: minimum, -23.13, mean -2.88, maximum 14.21 Coulombic values for B_Human_CHMP6_Q96FZ7_511fe_unrelaxed_rank_1_model_5.pdb_A SES surface #4.1: minimum, -17.29, mean -1.27, maximum 16.16 To also show corresponding color key, enter the above coulombic command and add key true > select clear > hide #!2 models > show #!2 models > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb"" Chain information for A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb #5 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb"" Chain information for A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb #6 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb"" Chain information for A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb #7 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb"" Chain information for A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb #8 --- Chain | Description A | No description available > close session > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb"" Chain information for A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb #1 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb"" Chain information for A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb #2 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb"" Chain information for A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb #3 --- Chain | Description A | No description available > open ""/Users/chaaban/Library/CloudStorage/OneDrive- > MRCLaboratoryofMolecularBiology/Documents/Carter > Lab/ESCRT/Sequences/AF/A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb"" Chain information for A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb #4 --- Chain | Description A | No description available > mmaker #2,3,4 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 A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A (#1) with A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb, chain A (#2), sequence alignment score = 441.1 RMSD between 80 pruned atom pairs is 0.949 angstroms; (across all 198 pairs: 20.445) Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A (#1) with A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb, chain A (#3), sequence alignment score = 363.8 RMSD between 53 pruned atom pairs is 1.083 angstroms; (across all 192 pairs: 27.603) Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A (#1) with A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb, chain A (#4), sequence alignment score = 305.6 RMSD between 73 pruned atom pairs is 1.008 angstroms; (across all 197 pairs: 25.672) > select clear Drag select of 241 residues > hide sel cartoons Drag select of 64 residues > hide sel cartoons Drag select of 2 residues > hide sel cartoons Drag select of 41 residues > hide sel cartoons Drag select of 20 residues > hide sel cartoons Drag select of 26 residues > hide sel cartoons Drag select of 21 residues Drag select of 11 residues > hide sel cartoons Drag select of 3 residues > hide sel cartoons > select #4/A:148-1000 574 atoms, 580 bonds, 75 residues, 1 model selected > hide sel cartoons > select clear Drag select of 426 residues > mmaker sel > matchmaker sel Missing required ""to"" argument > mmaker sel to #1 Must use different reference and match structures > hide #1 models Drag select of 319 residues > mmaker sel 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 A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A (#1) with A_Human_CHM2A_O43633_4b9b9_unrelaxed_rank_1_model_4.pdb, chain A (#2), sequence alignment score = 273.4 RMSD between 81 pruned atom pairs is 0.950 angstroms; (across all 107 pairs: 2.419) Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A (#1) with A_Human_CHM2B_Q9UQN3_5a6b5_unrelaxed_rank_1_model_1.pdb, chain A (#3), sequence alignment score = 241 RMSD between 65 pruned atom pairs is 0.954 angstroms; (across all 107 pairs: 5.443) Matchmaker A_Human_CHM1B_Q7LBR1_241ce_unrelaxed_rank_1_model_3.pdb, chain A (#1) with A_Human_CHMP3_Q9Y3E7_99010_unrelaxed_rank_1_model_3.pdb, chain A (#4), sequence alignment score = 188.5 RMSD between 72 pruned atom pairs is 1.018 angstroms; (across all 92 pairs: 3.105) > select clear > show #1 models Drag select of 426 residues > show sel surfaces > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Model Identifier: Mac14,5 Model Number: Z17J0018AB/A Chip: Unknown Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 64 GB System Firmware Version: 10151.81.1 OS Loader Version: 10151.81.1 Software: System Software Overview: System Version: macOS 14.3.1 (23D60) Kernel Version: Darwin 23.3.0 Time since boot: 3 days, 27 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL P2717H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes DELL P2722H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.3 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX