id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15353 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.1-arm64-arm-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 Current thread 0x00000001de145ec0 (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/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 264 in atom_residues File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 206 in molecule_from_atoms File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 100 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 100 in split_molecule File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/split.py"", line 63 in split 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/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent 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, 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""sharedCache"" : { ""base"" : 6571507712, ""size"" : 4055072768, ""uuid"" : ""f6dd368f-4e5e-3550-b73d-0d747cc10c97"" }, ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""a7a2c7b6040a187c00cef073c43acf89560dd23e"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""632c763c58740028737bfdd2"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""64a57d23fa6fd41b2353e2ae"" }, ""deploymentId"" : 240000034 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""5d51a80d-93ec-47e1-9027-675002e78e4a"", ""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000023 } ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 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/marla/Downloads/1vas.pdb 1vas.pdb title: Atomic model of A pyrimidine dimer specific excision repair enzyme complexed with A DNA substrate: structural basis for damaged DNA recognition [more info...] Chain information for 1vas.pdb #1 --- Chain | Description | UniProt A | T4 endonuclease V (E.C.3.1.25.1) | END5_BPT4 2-138 B | DNA (5'-D(*ap*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3') | C | DNA (5'-D(*TP*ap*GP*CP*GP*CP*ap*ap*CP*GP*CP*GP*A)-3') | > open /Users/marla/Downloads/3mr3.pdb 3mr3.pdb title: Human DNA polymerase η - DNA ternary complex with the 3'T of A CPD In the active site (TT1) [more info...] Chain information for 3mr3.pdb #2 --- Chain | Description | UniProt A | DNA polymerase η | POLH_HUMAN 1-432 P | DNA (5'-D(*CP*ap*GP*CP*GP*TP*CP*ap*T)-3') | T | DNA (5'-D(*CP*ap*(TTD)P*ap*TP*GP*ap*CP*GP*CP*T)-3') | Non-standard residues in 3mr3.pdb #2 --- DZ4 — 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion TTD — cis-syn cyclobutane thymine dimer ([(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-dihydroxy-15A,15B-dimethyl-7-oxido-13,15,16,18-tetraoxohexadecahydro-1H-1,4-epox Y-9,12-methano-6,8,11-trioxa-12A,14,17,18A-tetraaza-7-phosphacyclohexadeca[1,2,3,4-def]biphenylen-10-yl]methyl dihydrogen phosphate) > open /Users/marla/Downloads/3mr3.pdb 3mr3.pdb title: Human DNA polymerase η - DNA ternary complex with the 3'T of A CPD In the active site (TT1) [more info...] Chain information for 3mr3.pdb #3 --- Chain | Description | UniProt A | DNA polymerase η | POLH_HUMAN 1-432 P | DNA (5'-D(*CP*ap*GP*CP*GP*TP*CP*ap*T)-3') | T | DNA (5'-D(*CP*ap*(TTD)P*ap*TP*GP*ap*CP*GP*CP*T)-3') | Non-standard residues in 3mr3.pdb #3 --- DZ4 — 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine GOL — glycerol (glycerin; propane-1,2,3-triol) MG — magnesium ion TTD — cis-syn cyclobutane thymine dimer ([(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-dihydroxy-15A,15B-dimethyl-7-oxido-13,15,16,18-tetraoxohexadecahydro-1H-1,4-epox Y-9,12-methano-6,8,11-trioxa-12A,14,17,18A-tetraaza-7-phosphacyclohexadeca[1,2,3,4-def]biphenylen-10-yl]methyl dihydrogen phosphate) > hide #1 models > hide #!3 models > show #!3 models > select add #3 4250 atoms, 3920 bonds, 12 pseudobonds, 889 residues, 2 models selected > select subtract #3 Nothing selected > select add #3 4250 atoms, 3920 bonds, 12 pseudobonds, 889 residues, 2 models selected > select subtract #3 Nothing selected > hide #!3 models > close session > open /Users/marla/Downloads/1tez.pdb 1tez.pdb title: Complex between DNA and the DNA photolyase from anacystis nidulans [more info...] Chain information for 1tez.pdb #1 --- Chain | Description | UniProt A B C D | DNA photolyase; photoreactivating enzyme | PHR_SYNLE 2-475 I K | 5'-D(*ap*TP*CP*GP*GP*CP*T*(TCP)P*CP*GP*C)-3' | J L | 5'-D(P*CP*GP*ap*ap*GP*CP*CP*GP*A)-3' | M O | 5'-D(*TP*CP*GP*C)-3' | N P | 5'-D(P*GP*CP*CP*GP*A)-3' | Non-standard residues in 1tez.pdb #1 --- C — cytidine-5'-monophosphate FAD — flavin-adenine dinucleotide G — guanosine-5'-monophosphate HDF — 8-hydroxy-10-(D-ribo-2,3,4,5-tetrahydroxypentyl)-5-deazaisoalloxazine MG — magnesium ion TCP — 5'-methylthymidine > open /Users/marla/Downloads/7yc7.pdb 7yc7.pdb title: Dark, fully reduced structure of the mmcpdii-DNA complex As produced At swissfel [more info...] Chain information for 7yc7.pdb #2 --- Chain | Description A B | DNA photolyase C E | CPD photolesion containing DNA D F | complementary oligonucleotide to the CPD containing DNA Non-standard residues in 7yc7.pdb #2 --- FAD — flavin-adenine dinucleotide SO4 — sulfate ion TTD — cis-syn cyclobutane thymine dimer ([(3S,4S,9S,10R,12R,15AR,18BS,18CS)-3,7-dihydroxy-15A,15B-dimethyl-7-oxido-13,15,16,18-tetraoxohexadecahydro-1H-1,4-epox Y-9,12-methano-6,8,11-trioxa-12A,14,17,18A-tetraaza-7-phosphacyclohexadeca[1,2,3,4-def]biphenylen-10-yl]methyl dihydrogen phosphate) > hide #!1 models > select add #2 8468 atoms, 8510 bonds, 1233 residues, 1 model selected > hide sel cartoons > hide sel atoms > show sel cartoons > split #2 Split 7yc7.pdb (#2) into 6 models Chain information for 7yc7.pdb A #2.1 --- Chain | Description A | No description available Chain information for 7yc7.pdb B #2.2 --- Chain | Description B | No description available Chain information for 7yc7.pdb C #2.3 --- Chain | Description C | No description available Chain information for 7yc7.pdb D #2.4 --- Chain | Description D | No description available Chain information for 7yc7.pdb E #2.5 --- Chain | Description E | No description available Chain information for 7yc7.pdb F #2.6 --- Chain | Description F | No description available > hide #2.1 models > hide #2.3 models > hide #2.4 models > ui tool show ""Blast Protein"" > ui tool show ""Show Sequence Viewer"" > sequence chain #2.2/B Alignment identifier is 2.2/B > select #2.2/B:-4--3 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2.2/B:-4-10 114 atoms, 115 bonds, 15 residues, 1 model selected > select #2.2/B:462 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2.2/B:462 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2.2/B:-4 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:-4 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:234 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2.2/B:234-235 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2.2/B:239 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2.2/B:239-241 20 atoms, 19 bonds, 3 residues, 1 model selected > select #2.2/B:336-337 21 atoms, 21 bonds, 2 residues, 1 model selected > select #2.2/B:336-339 37 atoms, 37 bonds, 4 residues, 1 model selected > select #2.2/B:300 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:300-303 33 atoms, 32 bonds, 4 residues, 1 model selected > select #2.2/B:350-351 20 atoms, 20 bonds, 2 residues, 1 model selected > select #2.2/B:350-352 25 atoms, 25 bonds, 3 residues, 1 model selected > select #2.2/B:446-447 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2.2/B:446-451 47 atoms, 46 bonds, 6 residues, 1 model selected > select > #2.2/B:4-6,34-48,60-86,96-108,120-134,148-153,159-175,226-230,233-256,267-273,277-288,291-316,321-336,346-352,357-371,374-388,391-407,412-425,444-450,453-461 2149 atoms, 2193 bonds, 270 residues, 1 model selected > select #2.2/B:263 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:263-264 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2.2/B:252-253 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2.2/B:252-253 16 atoms, 16 bonds, 2 residues, 1 model selected > select #2.2/B:246 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2.2/B:246-247 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2.2/B:249 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:249-251 19 atoms, 18 bonds, 3 residues, 1 model selected > select #2.2/B:254 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2.2/B:254-256 24 atoms, 23 bonds, 3 residues, 1 model selected > select #2.2/B:260 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2.2/B:260-262 17 atoms, 16 bonds, 3 residues, 1 model selected > select #2.2/B:238 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2.2/B:238-239 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2.2/B:234 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2.2/B:234-236 19 atoms, 18 bonds, 3 residues, 1 model selected > select #2.2/B:240-241 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2.2/B:240-243 30 atoms, 29 bonds, 4 residues, 1 model selected > select #2.2/B:164 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2.2/B:164-165 18 atoms, 18 bonds, 2 residues, 1 model selected > select #2.2/B:167 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:167-169 25 atoms, 25 bonds, 3 residues, 1 model selected > select #2.2/B:160 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2.2/B:160-161 15 atoms, 15 bonds, 2 residues, 1 model selected > select #2.2/B:155 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2.2/B:155-158 40 atoms, 41 bonds, 4 residues, 1 model selected > select #2.2/B:233 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2.2/B:233-237 28 atoms, 27 bonds, 5 residues, 1 model selected > select #2.2/B:241 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:163-241 369 atoms, 384 bonds, 46 residues, 1 model selected > select > #2.2/B:4-6,34-48,60-86,96-108,120-134,148-153,159-175,226-230,233-256,267-273,277-288,291-316,321-336,346-352,357-371,374-388,391-407,412-425,444-450,453-461 2149 atoms, 2193 bonds, 270 residues, 1 model selected > select #2.2/B:229-230 21 atoms, 22 bonds, 2 residues, 1 model selected > select #2.2/B:229-232 33 atoms, 35 bonds, 4 residues, 1 model selected > select #2.2/B:235 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2.2/B:235-236 10 atoms, 9 bonds, 2 residues, 1 model selected > select #2.2/B:238-239 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2.2/B:238-240 18 atoms, 17 bonds, 3 residues, 1 model selected > select #2.2/B:245 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:245-247 21 atoms, 20 bonds, 3 residues, 1 model selected > select > #2.2/B:4-6,34-48,60-86,96-108,120-134,148-153,159-175,226-230,233-256,267-273,277-288,291-316,321-336,346-352,357-371,374-388,391-407,412-425,444-450,453-461 2149 atoms, 2193 bonds, 270 residues, 1 model selected > select #2.2/B:185-186 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2.2/B:185-224 50 atoms, 50 bonds, 7 residues, 1 model selected > select #2.2/B:-4 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2.2/B:-4--2 22 atoms, 22 bonds, 3 residues, 1 model selected > select #2.2/B:0 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2.2/B:0-70 534 atoms, 544 bonds, 71 residues, 1 model selected > select #2.2/B:435-436 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2.2/B:435-449 120 atoms, 121 bonds, 15 residues, 1 model selected > select add #2.2 3597 atoms, 3587 bonds, 548 residues, 1 model selected > select subtract #2.2 Nothing selected > close session > open /Users/marla/Downloads/3tbl.pdb 3tbl.pdb title: Structure of mono-ubiquitinated PCNA: implications for DNA polymerase switching and okazaki fragment maturation [more info...] Chain information for 3tbl.pdb #1 --- Chain | Description | UniProt A B C | proliferating cell nuclear antigen | PCNA_HUMAN 1-261 D E | ubiquitin | RS27A_HUMAN 1-76 > hide cartoons > hide atoms > show cartoons > split #1 ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle 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 M3 Pro 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: MacBook Pro Model Identifier: Mac15,7 Model Number: MRW13D/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1 (23B2073) Kernel Version: Darwin 23.1.0 Time since boot: 7 Tage, 5 Stunden und 14 Minuten Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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-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-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