id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15496 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-arm64-arm-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001e5f1d300 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/serialize.py"", line 70 in msgpack_deserialize File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 708 in restore File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/session.py"", line 1004 in open File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core_formats/__init__.py"", line 26 in open File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/open_command/cmd.py"", line 435 in 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Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local- > refine/RealSpaceRefine_2/trimmed-8flj- > AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- > renamed_real_space_refined_002.pdb Chain information for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available E | No description available G | No description available H | No description available > hbonds reveal true 1456 hydrogen bonds found > select add #1 21746 atoms, 22179 bonds, 1456 pseudobonds, 1844 residues, 2 models selected > style sel stick Changed 21746 atom styles > set bgColor white > lighting soft > select subtract #1 Nothing selected > select /A 9364 atoms, 9562 bonds, 838 pseudobonds, 1076 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:592 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:592 8 atoms, 7 bonds, 1 residue, 1 model selected > select > /A:2-7,32-36,58-64,70-77,91-93,414-418,446-450,474-478,511-513,541-545,572-576,603-606,642-647,652-657,687-690,723-725,728-736,759-766,813-820,834-837,865-868,979-986,994-1000,1003-1006,1011-1013,1022-1024,1055-1058,1064-1067,1071-1074 1477 atoms, 1487 bonds, 94 pseudobonds, 150 residues, 2 models selected > select /A:576 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:576-579 32 atoms, 31 bonds, 4 residues, 1 model selected > select > /A:2-7,32-36,58-64,70-77,91-93,414-418,446-450,474-478,511-513,541-545,572-576,603-606,642-647,652-657,687-690,723-725,728-736,759-766,813-820,834-837,865-868,979-986,994-1000,1003-1006,1011-1013,1022-1024,1055-1058,1064-1067,1071-1074 1477 atoms, 1487 bonds, 94 pseudobonds, 150 residues, 2 models selected > select > /A:10-22,38-52,79-82,109-122,125-128,130-137,149-161,167-175,183-187,208-219,231-236,243-246,253-260,267-269,271-286,290-298,301-320,349-364,367-373,381-384,390-412,426-437,457-467,484-496,500-502,524-527,531-538,546-548,550-552,562-568,578-580,583-585,587-598,612-631,660-679,699-720,740-753,772-785,793-797,800-808,822-824,842-851,872-875,899-902,905-909,914-917,929-938,953-956,960-963,966-970,1008-1010,1030-1041,1045-1052 4099 atoms, 4123 bonds, 343 pseudobonds, 475 residues, 2 models selected > select /A 9364 atoms, 9562 bonds, 838 pseudobonds, 1076 residues, 2 models selected > select /A 9364 atoms, 9562 bonds, 838 pseudobonds, 1076 residues, 2 models selected > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/supp.movies/3-model- > comparison.cxs ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/supp.movies/3-model- > comparison.cxs Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size 324,324,324, pixel 1.1, shown at level 0.0681, step 1, values float32 Log from Thu Jun 6 16:35:37 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open /Users/whenriques/Downloads/3models+J1277-003-map_colored_sequences- > corrected.cxs Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size 324,324,324, pixel 1.1, shown at level 0.0681, step 1, values float32 Log from Wed Jun 5 14:28:52 2024UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary- > sessions/3models+J1277-003-map_colored_sequences-corrected.cxs"" Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size 324,324,324, pixel 1.1, shown at level 0.0681, step 1, values float32 Log from Tue Jun 4 10:22:47 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/20240410-isolde-refinement- > cas1-cdef-cas2H-cas3-GH-deleteG96HA2_real_space_refined_017.pdb"" Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017.pdb #1 --- Chain | Description A B C D | No description available E F I J | No description available G H | No description available > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/capture_jerry-modded.pdb"" Chain information for capture_jerry-modded.pdb #2 --- Chain | Description A B | No description available C D E F | No description available > save ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/20240410-isolde-refinement- > cas1-cdef-cas2H-cas3-GH-deleteG96HA2_real_space_refined_017_jerry- > modded.pdb"" models #2 > close > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/8flj-AFrepeat-dna-added- > AFCas3-prelim-equilibration_real_space_refined_001-dna-bonds-added_Jerry- > modded.pdb"" Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb #1 --- Chain | Description A B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K L | No description available M | No description available > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/capture_jerry-modded.pdb"" Chain information for capture_jerry-modded.pdb #2 --- Chain | Description A B | No description available C D E F | No description available > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/20240410-isolde-refinement- > cas1-cdef-cas2H-cas3-GH-deleteG96HA2_real_space_refined_017_jerry- > modded.pdb"" Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb #3 --- Chain | Description A B | No description available C D E F | No description available > open C:/Users/jarre/Downloads/cryosparc_P19_J1277_003_volume_map.mrc Opened cryosparc_P19_J1277_003_volume_map.mrc as #4, grid size 324,324,324, pixel 1.1, shown at level 0.0681, step 2, values float32 > vop flip #4 Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size 324,324,324, pixel 1.1, shown at step 1, values float32 > close #4 > set bgColor white > graphics silhouettes true > lighting shadows true > lighting soft fillDirection -.1,.1,-.25 fillIntensity 0.1 direction -0, .1, > -.2 intensity 0.2 multiShadow 128 > material specularReflectivity 0.1 > cartoon style protein xsection oval modeHelix default > hide atoms > show cartoons > color #2/g,h #f69320ff > color #1,2,3/a:1-94/b:1-94 #d799c4 > color #1,2,3/a:95-end/b:95-end #6d8fc9ff > color #1,2,3/f,e #c2b59bff > color #1,2,3/c,d #9c857a > color #1/g:1-27/h:1-27 #f69320ff > color #1/g:28-end/h:28-56 #92278f > color #1/i/h:57-end #939598 > color #1/m,k #d91b5d > color #1/l,j #a51e23 > hide #!5 models > lighting simple > hide #3 models > hide #2 models > save ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/3models+_colored_sequences- > corrected .cxs"" includeMaps true ——— End of log from Tue Jun 4 10:22:47 2024 ——— opened ChimeraX session > split Split 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb (#1) into 13 models Split capture_jerry-modded.pdb (#2) into 6 models Split 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb (#3) into 6 models Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb A #1.1 --- Chain | Description A | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb B #1.2 --- Chain | Description B | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb C #1.3 --- Chain | Description C | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb D #1.4 --- Chain | Description D | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb E #1.5 --- Chain | Description E | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb F #1.6 --- Chain | Description F | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb G #1.7 --- Chain | Description G | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb H #1.8 --- Chain | Description H | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb I #1.9 --- Chain | Description I | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb J #1.10 --- Chain | Description J | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb K #1.11 --- Chain | Description K | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb L #1.12 --- Chain | Description L | No description available Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb M #1.13 --- Chain | Description M | No description available Chain information for capture_jerry-modded.pdb A #2.1 --- Chain | Description A | No description available Chain information for capture_jerry-modded.pdb B #2.2 --- Chain | Description B | No description available Chain information for capture_jerry-modded.pdb C #2.3 --- Chain | Description C | No description available Chain information for capture_jerry-modded.pdb D #2.4 --- Chain | Description D | No description available Chain information for capture_jerry-modded.pdb E #2.5 --- Chain | Description E | No description available Chain information for capture_jerry-modded.pdb F #2.6 --- Chain | Description F | No description available Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb A #3.1 --- Chain | Description A | No description available Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb B #3.2 --- Chain | Description B | No description available Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb C #3.3 --- Chain | Description C | No description available Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb D #3.4 --- Chain | Description D | No description available Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb E #3.5 --- Chain | Description E | No description available Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb F #3.6 --- Chain | Description F | No description available > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #!1 models > hide #!2 models > show #!2 models > show #2.1 models > show #2.2 models > show #2.3 models > show #3.1 models > show #3.2 models > close > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/current-models/8flj-AFrepeat- > dna-added-AFCas3-prelim-equilibration_real_space_refined_001-dna-bonds- > added_Jerry-modded.pdb"" Chain information for 8flj-AFrepeat-dna-added-AFCas3-prelim- equilibration_real_space_refined_001-dna-bonds-added_Jerry-modded.pdb #1 --- Chain | Description A B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K L | No description available M | No description available > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/current-models/prespacer- > bound_jerry-modded.pdb"" prespacer-bound_jerry-modded.pdb title: Alphafold monomer V2.0 prediction for crispr-associated nuclease/helicase CAS3 subtype I-F/ypest (Q02ML8) [more info...] Chain information for prespacer-bound_jerry-modded.pdb #2 --- Chain | Description | UniProt A | crispr-associated nuclease/helicase CAS3 subtype I-F/ypest | CAS3_PSEAB 1-1076 B | No description available | C D E F | No description available | G | No description available | H | No description available | > open ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary-sessions/current-models/20240410-isolde- > refinement-cas1-cdef-cas2H-cas3-GH- > deleteG96HA2_real_space_refined_017_jerry-modded.pdb"" Chain information for 20240410-isolde-refinement-cas1-cdef-cas2H-cas3-GH- deleteG96HA2_real_space_refined_017_jerry-modded.pdb #3 --- Chain | Description A B | No description available C D E F | No description available > set bgColor white > graphics silhouettes true > lighting shadows true > lighting soft fillDirection -.1,.1,-.25 fillIntensity 0.1 direction -0, .1, > -.2 intensity 0.2 multiShadow 128 > material specularReflectivity 0.1 > cartoon style protein xsection oval modeHelix default > hide atoms > show cartoons > color #2/g,h #f69320ff > color #1,2,3/a:1-94/b:1-94 #d799c4 > color #1,2,3/a:95-end/b:95-end #6d8fc9ff > color #1,2,3/f,e #c2b59bff > color #1,2,3/c,d #9c857a > color #1/g:1-27/h:1-27 #f69320ff > color #1/g:28-end/h:28-56 #92278f > color #1/i/h:57-end #939598 > color #1/m,k #d91b5d > color #1/l,j #a51e23 > hide #2 models > hide #3 models > show #3 models > show #2 models > open C:/Users/jarre/Downloads/cryosparc_P19_J1277_003_volume_map.mrc Opened cryosparc_P19_J1277_003_volume_map.mrc as #4, grid size 324,324,324, pixel 1.1, shown at level 0.0681, step 2, values float32 > vop flip #4 Opened cryosparc_P19_J1277_003_volume_map.mrc z flip as #5, grid size 324,324,324, pixel 1.1, shown at step 1, values float32 > close #4 > save ""C:/Users/jarre/Documents/MSU/Wiedenheft Lab/Projects/1-F integration > complex/MyIntegrationMovie/Primary- > sessions/3models+J1277-003-map_colored_sequences-corrected.cxs"" includeMaps > true ——— End of log from Wed Jun 5 14:28:52 2024 ——— opened ChimeraX session > save /Users/whenriques/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/supp.movies/3-model- > comparison.cxs includeMaps true ——— End of log from Thu Jun 6 16:35:37 2024 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MJ123LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 17 days, 22 hours, 4 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal BenQ GW2760HS: 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: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 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: 1.1.1 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: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 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: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Core duplicate all ChimeraX