id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10309 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6rc202304150037 (2023-04-15 00:37:23 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 0x00007ff84f853b40 (most recent call first): File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/numpy/core/_internal.py"", line 251 in __init__ File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py"", line 322 in pointer File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molc.py"", line 240 in set_cvec_pointer File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py"", line 122 in __init__ File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molarray.py"", line 382 in __init__ File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py"", line 2186 in process_changes File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/molobject.py"", line 2191 in changes File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/atomic/changes.py"", line 25 in check_for_changes File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 58 in draw_new_frame File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6-rc2023.04.15.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-12-08 13:15:38.00 +0100"",""app_version"":""1.6.0"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.1.1 (23B81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""8CE7EFF0-F16F-49C3-BCA0-2345DF76FE26""} { ""uptime"" : 280000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,2"", ""coalitionID"" : 5276, ""osVersion"" : { ""train"" : ""macOS 14.1.1"", ""build"" : ""23B81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-12-08 13:15:36.9641 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""8CE7EFF0-F16F-49C3-BCA0-2345DF76FE26"", ""pid"" : 90015, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-12-08 12:22:44.3893 +0100"", ""procStartAbsTime"" : 285277527570301, ""procExitAbsTime"" : 288450010184216, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6-rc2023.04.15.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D4B84B47-846E-5515-A255-E5818514FA5B"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""9B98626C-34AA-4037-BF37-43F9688AEC0C"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 13004, ""bridgeVersion"" : {""build"":""21P1069"",""train"":""8.1""}, ""sleepWakeUUID"" : ""3E428BA1-6870-4426-B693-34DB2CB0F205"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > ui tool show AlphaFold > alphafold predict > VKLENILIKNGGGHGRDTYGASGKIAKGDAKKSDSDVYSIDEIL,MSFFQFIKGDERKMNQHVKVTFDFTNYNYGTYDLAVPAYLPIKNLIALVLDSLDISIFDVNTQIKVMTKGQLLVENDRLIDYQIADGDILKLL Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. Running AlphaFold prediction AlphaFold prediction finished Results in /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_78 > open > /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_78/best_model.pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available B | No description available > alphafold predict > VKLENILIKNGGGHGRDTYGASGKIAKGDAKKSDSDVYSIDEIL,DKTIYMINDYGQLQAINKDLS Running AlphaFold prediction AlphaFold prediction finished Results in /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79 > open > /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > hide #2 models > show #2 models > hide #1 models > alphafold pae #2 file > /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79/best_model_pae.json > color #2/A:5-37 lime > color #2/B:8-17 lime > color #2/A:4-37 magenta > alphafold pae #2 colorDomains true > ui tool show ""Show Sequence Viewer"" > sequence chain #2/B Alignment identifier is 2/B > select #2/B:21 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/B 170 atoms, 171 bonds, 21 residues, 1 model selected > color sel magenta > select #2/A 325 atoms, 327 bonds, 44 residues, 1 model selected > color sel light gray > select clear > save ""/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure > related/bioinformatic/SAO_YukB_Btb_vs_Toxin_prepretoxinmotiv.cxs"" > open ""/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure > related/SAO_YukB_BtB_YukD_PPTXmotv.cxs"" opened ChimeraX session > close > open ""/Users/gabrielumajioka/Desktop/project T7SS /T7SS structure > related/SAO_YukB_BtB_YukD_PPTXmotv.cxs"" opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > sequence chain /B Alignment identifier is 1/B > sequence chain /C Alignment identifier is 1/C > open > /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_79/best_model.pdb Chain information for best_model.pdb #2 --- Chain | Description A | No description available B | No description available > hide #2 models > show #2 models > select add #2 665 atoms, 669 bonds, 86 residues, 2 models selected > hide #1 models > select add #1 1782 atoms, 1802 bonds, 227 residues, 2 models selected > select subtract #1 495 atoms, 498 bonds, 65 residues, 1 model selected > show #1 models > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-17.774,0,1,0,34.757,0,0,1,-12.016 > select #2/A 325 atoms, 327 bonds, 44 residues, 1 model selected > color sel white > select #2/B 170 atoms, 171 bonds, 21 residues, 1 model selected > color sel magenta > select clear > select add #2 495 atoms, 498 bonds, 65 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.26188,0.91932,-0.29373,-18.175,-0.87555,-0.35434,-0.32842,40.457,-0.406,0.17117,0.8977,-11.771 > view matrix models > #2,-0.37625,0.88556,0.27243,-16.049,-0.92643,-0.36366,-0.097363,41.322,0.012853,-0.28902,0.95724,-11.258 > view matrix models > #2,0.066154,0.89172,0.44773,-16.737,-0.98009,-0.026126,0.19685,41.279,0.18723,-0.45184,0.87223,-11.468 > view matrix models > #2,-0.076723,0.82126,-0.56537,-19.184,-0.97598,-0.17782,-0.12586,40.778,-0.2039,0.54213,0.81518,-13.751 > view matrix models > #2,-0.39737,0.6668,-0.63045,-18.019,-0.87009,-0.4921,0.02794,41.958,-0.29162,0.55965,0.77573,-13.688 > view matrix models > #2,-0.64379,0.56386,-0.5173,-16.682,-0.73416,-0.64576,0.20979,42.629,-0.21576,0.51484,0.82969,-13.588 > view matrix models > #2,-0.60641,0.70218,-0.37312,-16.789,-0.79507,-0.54237,0.27149,42.65,-0.011732,0.46128,0.88717,-13.796 > view matrix models > #2,-0.42776,0.79932,-0.42204,-17.73,-0.90382,-0.37208,0.21136,42.22,0.011915,0.47186,0.88159,-13.911 > view matrix models > #2,-0.66462,0.63827,-0.38846,-16.474,-0.74717,-0.56476,0.3504,42.83,0.0042678,0.52313,0.85224,-14.142 > select add #1 1782 atoms, 1802 bonds, 227 residues, 2 models selected > select subtract #2 1287 atoms, 1304 bonds, 162 residues, 1 model selected > view matrix models > #1,0.91137,-0.24024,-0.33419,0.098075,0.1648,0.95704,-0.23855,-0.3079,0.37715,0.16233,0.91182,-0.6378 > view matrix models > #1,0.94814,0.047907,-0.31421,0.26087,-0.081321,0.99224,-0.094109,0.20005,0.30726,0.11478,0.94468,-0.54038 > view matrix models > #1,0.94912,0.048674,-0.31112,0.25837,-0.081314,0.99236,-0.092808,0.19969,0.30423,0.11338,0.94583,-0.53549 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.94912,0.048674,-0.31112,7.0268,-0.081314,0.99236,-0.092808,-20.437,0.30423,0.11338,0.94583,-6.9056 > ui tool show AlphaFold > help help:user/tools/alphafold.html > alphafold predict > MSFFQFIKGDERKMNQHVKVTFDFTNYNYGTYDLAVPAYLPIKNLIALVLDSLDISIFDVNTQIKVMTKGQLLVENDRLIDYQIADGDILKLL,VKLENILIKNGGGHGRDTYGASGKIAKGDAKKSDSDVYSIDEIL Running AlphaFold prediction AlphaFold prediction finished Results in /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_80 > open > /Users/gabrielumajioka/Downloads/ChimeraX/AlphaFold/prediction_80/best_model.pdb Chain information for best_model.pdb #3 --- Chain | Description A | No description available B | No description available > select add #2 1782 atoms, 1802 bonds, 227 residues, 2 models selected > select subtract #2 1287 atoms, 1304 bonds, 162 residues, 1 model selected > select add #3 2368 atoms, 2400 bonds, 299 residues, 2 models selected > select subtract #1 1081 atoms, 1096 bonds, 137 residues, 1 model selected > view matrix models #3,1,0,0,14.872,0,1,0,-47.034,0,0,1,15.977 > view matrix models #3,1,0,0,28.952,0,1,0,-73.398,0,0,1,0.38853 > select #3/A 756 atoms, 769 bonds, 93 residues, 1 model selected > color sel orange > select clear > select #3/B 325 atoms, 327 bonds, 44 residues, 1 model selected > color sel white > select clear > select add #3 1081 atoms, 1096 bonds, 137 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.99773,-0.065708,0.014415,29.151,0.066419,0.99621,-0.056137,-73.156,-0.010672,0.056968,0.99832,0.17168 > view matrix models > #3,0.75751,-0.4448,0.47784,28.896,0.26977,0.87982,0.39132,-74.095,-0.59447,-0.16753,0.78647,1.3904 > view matrix models > #3,0.58285,-0.69781,0.41635,29.959,0.6299,0.71169,0.31101,-72.976,-0.51334,0.080986,0.85436,0.26742 > view matrix models > #3,0.3252,-0.90016,0.28975,31,0.5199,0.42613,0.74035,-73.395,-0.7899,-0.09012,0.60657,1.5847 > view matrix models > #3,0.48592,-0.82392,0.2916,30.799,0.17803,0.41995,0.88991,-74.074,-0.85568,-0.38052,0.35075,3.5056 > view matrix models > #3,0.35778,-0.88895,0.28595,30.989,0.45721,0.43377,0.7764,-73.582,-0.81422,-0.14704,0.56163,1.937 > view matrix models > #3,0.63381,-0.35183,0.68885,27.763,-0.76328,-0.42871,0.48333,-70.044,0.12527,-0.83212,-0.54026,8.7828 > view matrix models > #3,0.77879,0.43754,0.44949,25.654,-0.62594,0.49526,0.60242,-73.869,0.04097,-0.75052,0.65958,4.4021 > view matrix models > #3,0.31191,-0.1341,0.9406,25.903,-0.79677,0.50236,0.33583,-73.103,-0.51756,-0.85419,0.049845,6.5107 > view matrix models > #3,0.17202,-0.43846,0.88214,27.172,-0.19515,0.86257,0.46679,-74.556,-0.96557,-0.25244,0.062812,3.9199 > view matrix models > #3,-0.53719,-0.65566,0.53059,28.758,-0.50289,0.754,0.42259,-74.176,-0.67715,-0.039816,-0.73477,5.9557 > view matrix models > #3,-0.74138,-0.62118,-0.25396,31.136,-0.66958,0.71006,0.21789,-73.422,0.044978,0.33159,-0.94235,5.6664 > view matrix models > #3,-0.78122,-0.60213,-0.16473,30.742,-0.61441,0.78833,0.03226,-73.064,0.11043,0.12641,-0.98581,6.6293 > view matrix models > #3,-0.85682,-0.51497,-0.025656,29.9,-0.48072,0.81585,-0.3214,-71.904,0.18644,-0.26305,-0.9466,8.0207 > view matrix models > #3,-0.89319,-0.44888,0.026897,29.452,-0.40268,0.77176,-0.49217,-71.119,0.20017,-0.45043,-0.87008,8.4836 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6rc202304150037 (2023-04-15) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.1.28 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. 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: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2,3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0) OS Loader Version: 580~743 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 9 days, 3 hours, 3 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG UltraFine: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 806NTKF1F589 Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: Thunderbolt/DisplayPort 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 ChimeraX-AddH: 2.2.4 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-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: 1.6rc202304150037 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-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: 2.7.1 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: 1.10.2 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: 6.4.1 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 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.2.0 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: 6.2 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 can't reproduce all ChimeraX