id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17181 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.3-arm64-arm-64bit ChimeraX Version: 1.8rc202405282004 (2024-05-28 20:04:22 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000030b8a7000 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001f6750840 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py"", line 576 in __init__ File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 1616 in remove_deleted_pointers File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 134 in __init__ File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 1190 in __init__ File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2246 in process_changes File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2251 in changes File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 36 in check_for_changes File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py"", line 77 in File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3318 in command_trigger File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 144 in __exit__ File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3203 in run File ""/Applications/ChimeraX-1.8-rc2024.05.28.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-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 535 in run File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 592 in run_expanded_command File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 338 in run File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 419 in run_shortcut File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 401 in try_shortcut File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py"", line 1386 in run_provider File ""/Applications/ChimeraX-1.8-rc2024.05.28.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-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1306 in run_provider File ""/Applications/ChimeraX-1.8-rc2024.05.28.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-1.8-rc2024.05.28.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-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 307 in event_loop File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8-rc2024.05.28.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 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, 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kernel 1558K 1 \nshared memory 3200K 25 \n=========== ======= ======= \nTOTAL 5.2G 6222 \nTOTAL, minus reserved VM space 5.0G 6222 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""22ab1b79c0955c4662d59d4d6dae34bb476819b8"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67181b10c68c361a728c7cfa"", ""factorPackIds"" : { }, ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lassa_wt_endo_5j1n_2copies/fold_lassa_wt_endo_5j1n_2copies_model_0.cif"" Chain information for fold_lassa_wt_endo_5j1n_2copies_model_0.cif #1 --- Chain | Description A B | . > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lassa_pross_des3_2copies/fold_lassa_pross_des3_2copies_model_0.cif"" Chain information for fold_lassa_pross_des3_2copies_model_0.cif #2 --- Chain | Description A B | . > matchmaker #1 to #2 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_lassa_pross_des3_2copies_model_0.cif, chain A (#2) with fold_lassa_wt_endo_5j1n_2copies_model_0.cif, chain A (#1), sequence alignment score = 860 RMSD between 170 pruned atom pairs is 0.507 angstroms; (across all 171 pairs: 0.562) > set bgColor white > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lassa_wt_endo_5j1n/fold_lassa_wt_endo_5j1n_model_0.cif"" Chain information for fold_lassa_wt_endo_5j1n_model_0.cif #3 --- Chain | Description A | . > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lassa_pross_des3/fold_lassa_pross_des3_model_0.cif"" Chain information for fold_lassa_pross_des3_model_0.cif #4 --- Chain | Description A | . > hide #2 models > hide #1 models > matchmaker #3 to #4 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_lassa_pross_des3_model_0.cif, chain A (#4) with fold_lassa_wt_endo_5j1n_model_0.cif, chain A (#3), sequence alignment score = 854.2 RMSD between 155 pruned atom pairs is 0.947 angstroms; (across all 171 pairs: 1.493) > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B #4/A Alignment identifier is 1 > sequence chain #1/A #1/B #3/A Alignment identifier is 2 > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lasv_pross3_s107n/fold_lasv_pross3_s107n_model_0.cif"" Chain information for fold_lasv_pross3_s107n_model_0.cif #5 --- Chain | Description A | . > matchmaker #5 to #4 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_lassa_pross_des3_model_0.cif, chain A (#4) with fold_lasv_pross3_s107n_model_0.cif, chain A (#5), sequence alignment score = 913 RMSD between 173 pruned atom pairs is 0.555 angstroms; (across all 176 pairs: 0.800) > hide #3 models > ui mousemode right select > select #5/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:109 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:108 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #5/A:108 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #4/A:109 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/A:110 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #5/A:110 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lasv_pross3_s107n_2copies/fold_lasv_pross3_s107n_2copies_model_0.cif"" Chain information for fold_lasv_pross3_s107n_2copies_model_0.cif #6 --- Chain | Description A B | . > matchmaker #6 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_lassa_wt_endo_5j1n_2copies_model_0.cif, chain A (#1) with fold_lasv_pross3_s107n_2copies_model_0.cif, chain A (#6), sequence alignment score = 857.9 RMSD between 171 pruned atom pairs is 0.454 angstroms; (across all 171 pairs: 0.454) > hide #4 models > hide #5 models > hide #6 models > show #1 models > show #2 models > show #6 models > hide #2 models > show #3 models > show #4 models > hide #6 models > hide #1 models > select clear > open /Users/simeonbabarinde/Desktop/March_25_SSRL/ref9/B5_P61_210_009.pdb > format pdb Chain information for B5_P61_210_009.pdb #7 --- Chain | Description A | No description available B | No description available 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show ""Show Sequence Viewer"" > sequence chain #7/A Alignment identifier is 7/A > sequence chain #1/A #1/B #3/A Alignment identifier is 1 > sequence chain #2/A #2/B #4/A Alignment identifier is 2 > close > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lassa_wt_endo_5j1n/fold_lassa_wt_endo_5j1n_model_0.cif"" Chain information for fold_lassa_wt_endo_5j1n_model_0.cif #1 --- Chain | Description A | . > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lassa_pross_des3/fold_lassa_pross_des3_model_0.cif"" Chain information for fold_lassa_pross_des3_model_0.cif #2 --- Chain | Description A | . > matchmaker #2 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_lassa_wt_endo_5j1n_model_0.cif, chain A (#1) with fold_lassa_pross_des3_model_0.cif, chain A (#2), sequence alignment score = 854.2 RMSD between 155 pruned atom pairs is 0.947 angstroms; (across all 171 pairs: 1.493) > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A:171 13 atoms, 13 bonds, 1 residue, 1 model selected > select #1/A 1375 atoms, 1397 bonds, 171 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:176 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A 1416 atoms, 1438 bonds, 176 residues, 1 model selected > open 5J1N 5j1n title: Lassa virus L protein cap-snatching endonuclease. Bound to one manganese ion [more info...] Chain information for 5j1n #3 --- Chain | Description | UniProt A | RNA-directed RNA polymerase L | Q6GWS6_9VIRU 1-174 Non-standard residues in 5j1n #3 --- MN3 — manganese (III) ion MPD — (4S)-2-methyl-2,4-pentanediol 37 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > matchmaker #3 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_lassa_wt_endo_5j1n_model_0.cif, chain A (#1) with 5j1n, chain A (#3), sequence alignment score = 877.5 RMSD between 155 pruned atom pairs is 0.957 angstroms; (across all 171 pairs: 1.346) > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > select #3/A:61-62,90-94,97-105,136-144 199 atoms, 199 bonds, 25 residues, 1 model selected > select clear > select #3/A:0-170 1373 atoms, 1395 bonds, 171 residues, 1 model selected > close #1 > select #2/A:58-59 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:58-59 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:58 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:58 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:56 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > color sel byhetero > select #2/A:58 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero > open ""/Users/simeonbabarinde/Desktop/PhD Projects/Endonuclease > project/fold_lasv_wt_5j1n/fold_lasv_wt_5j1n_model_0.cif"" Chain information for fold_lasv_wt_5j1n_model_0.cif #1 --- Chain | Description A | . > matchmaker #3 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_lasv_wt_5j1n_model_0.cif, chain A (#1) with 5j1n, chain A (#3), sequence alignment score = 908.3 RMSD between 162 pruned atom pairs is 0.922 angstroms; (across all 171 pairs: 1.074) > matchmaker #2 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_lasv_wt_5j1n_model_0.cif, chain A (#1) with fold_lassa_pross_des3_model_0.cif, chain A (#2), sequence alignment score = 891.6 RMSD between 164 pruned atom pairs is 0.808 angstroms; (across all 175 pairs: 1.261) > select #1/A:57 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:57 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:2-17,22-32,37-60,71-78,111-135,156-175 867 atoms, 874 bonds, 104 residues, 1 model selected > select #2/A:159 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:159 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:157 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select #3/A:166 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A:167 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #1/A:167 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero > select #3/A:166 6 atoms, 5 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero > select #2/A:168 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > color sel red > select #2/A:159 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero > select clear > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > color sel red > color sel byhetero ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8rc202405282004 (2024-05-28) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15G001WGLL/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 11881.81.2 OS Loader Version: 11881.81.2 Software: System Software Overview: System Version: macOS 15.3 (24D60) Kernel Version: Darwin 24.3.0 Time since boot: 5 days, 11 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2419H: Resolution: 1080 x 1920 UI Looks like: 1080 x 1920 @ 60.00Hz Mirror: Off Online: Yes Rotation: 90 LG ULTRAFINE: Resolution: 4096 x 2304 UI Looks like: 2048 x 1152 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 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: 2.2.4 ChimeraX-Clipper: 0.23.0 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: 1.8rc202405282004 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 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: 1.1.1 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.13 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.2 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.52.4 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 MolecularDynamicsViewer: 1.4 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.45 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.12.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Core duplicate all ChimeraX