id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16123 Crash in Qt redraw after screen disconnect chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit 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 0x0000000200b5d2c0 (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/save_command/dialog.py"", line 39 in display File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py"", line 127 in show_save_file_dialog File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py"", line 116 in File ""/Applications/ChimeraX-1.6.1.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-1.6.1.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-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.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"":""2024-10-11 15:26:53.00 -0700"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.2.1 (22D68)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""13C00820-787A-428A-99E6-DBEAB6E80419""} { ""uptime"" : 280000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 379343813, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,9"", ""coalitionID"" : 55424, ""osVersion"" : { ""train"" : ""macOS 13.2.1"", ""build"" : ""22D68"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-10-11 15:22:50.1374 -0700"", ""incident"" : ""13C00820-787A-428A-99E6-DBEAB6E80419"", ""pid"" : 44219, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-10-10 18:31:25.3037 -0700"", ""procStartAbsTime"" : 6381774426100, ""procExitAbsTime"" : 6786744790867, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""4FC7D034-2ACA-5BED-8456-AEF1ED111E4F"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""49A7EAB0-B44A-F787-66C8-922581B31ABB"", ""throttleTimeout"" : 2147483647, ""wakeTime"" : 3846, ""sleepWakeUUID"" : ""6F25391E-09F7-4EE4-9499-03499A6EA9A1"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x24 is not in any region. 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""\/usr\/lib\/system\/libsystem_notify.dylib"", ""name"" : ""libsystem_notify.dylib"" } ], ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112e3d2fc54bc3389840661"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""648b9b0febdf9e3e398fa6b5"" }, ""deploymentId"" : 240000478 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 5W1K Summary of feedback from opening 5W1K fetched from pdb --- note | Fetching compressed mmCIF 5w1k from http://files.rcsb.org/download/5w1k.cif 5w1k title: JUNV GP1 CR1-10 Fab CR1-28 Fab complex [more info...] Chain information for 5w1k #1 --- Chain | Description | UniProt A F K S | CR1-28 Fab light chain | IGK_HUMAN 104-207 B G L T | CR1-28 Fab heavy chain | S6C4R2_HUMAN 127-226 C H M N | CR1-10 Fab light chain | Q6PIL8_HUMAN 107-214 D I O Q | CR1-10 Fab heavy chain | S6B2B6_HUMAN 127-226 E J P R | Pre-glycoprotein polyprotein GP complex | GLYC_JUNIN 87-228 Non-standard residues in 5w1k #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 5w1k mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > delete /D/I/O > delete /C/H/M > close > open 5W1K format mmcif fromDatabase pdb 5w1k title: JUNV GP1 CR1-10 Fab CR1-28 Fab complex [more info...] Chain information for 5w1k #1 --- Chain | Description | UniProt A F K S | CR1-28 Fab light chain | IGK_HUMAN 104-207 B G L T | CR1-28 Fab heavy chain | S6C4R2_HUMAN 127-226 C H M N | CR1-10 Fab light chain | Q6PIL8_HUMAN 107-214 D I O Q | CR1-10 Fab heavy chain | S6B2B6_HUMAN 127-226 E J P R | Pre-glycoprotein polyprotein GP complex | GLYC_JUNIN 87-228 Non-standard residues in 5w1k #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 5w1k mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > delete /A/B/P/O/N > ui mousemode right select Drag select of 1769 atoms > delete sel Drag select of 13786 atoms, 72 bonds, 33 pseudobonds > delete sel > delete /W Drag select of 45 atoms > select add #1 7787 atoms, 7995 bonds, 1015 residues, 1 model selected > select subtract #1 Nothing selected > ui mousemode right ""translate selected models"" > set bgColor white > lighting soft > show cartoons > hide atoms > cartoon style thickness 1.2 > open 8P4T 8p4t title: The spike complex of the Lujo Virus [more info...] Chain information for 8p4t #2 --- Chain | Description | UniProt A B C | Glycoprotein | C5ILC1_9VIRU 59-221 SA SB SC | Glycoprotein | C5ILC1_9VIRU -2-55 a b c | Glycoprotein | C5ILC1_9VIRU 222-454 Non-standard residues in 8p4t #2 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NA — sodium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > mmaker #2 to #1/E 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 5w1k, chain E (#1) with 8p4t, chain A (#2), sequence alignment score = 98.7 RMSD between 50 pruned atom pairs is 1.263 angstroms; (across all 119 pairs: 4.347) > hide atoms > show atoms > show cartoons > hide atoms > cartoon style thickness 1.2 > color #2 grey > color #1 purple > ui tool show ""Side View"" > graphics silhouettes true > mmaker #2 to #1/B No 'to' model specified > mmaker #1/E to #2/B 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 8p4t, chain B (#2) with 5w1k, chain E (#1), sequence alignment score = 98.7 RMSD between 50 pruned atom pairs is 1.263 angstroms; (across all 119 pairs: 4.347) > mmaker #1/E to #2/C 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 8p4t, chain C (#2) with 5w1k, chain E (#1), sequence alignment score = 98.7 RMSD between 50 pruned atom pairs is 1.263 angstroms; (across all 119 pairs: 4.347) > open > /Users/tgewering/Downloads/cryosparc_P64_J902_class_00_00040_volume_sharp.mrc Opened cryosparc_P64_J902_class_00_00040_volume_sharp.mrc as #3, grid size 64,64,64, pixel 5.28, shown at level 0.109, step 1, values float32 > ui tool show ""Side View"" > select add #3 4 models selected > view matrix models #3,1,0,0,-126.37,0,1,0,-121.29,0,0,1,-55.903 > view matrix models #3,1,0,0,-198.23,0,1,0,-233.28,0,0,1,-120.28 > volume #3 level 0.4641 > hide #!2 models > view matrix models #3,1,0,0,-214.77,0,1,0,-249.4,0,0,1,-127.75 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.26183,-0.39834,-0.87907,214.19,0.63753,-0.75522,0.15233,-73.699,-0.72457,-0.52054,0.4517,177.1 > fitmap #1 inMap #3 Fit molecule 5w1k (#1) to map cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) using 7787 atoms average map value = 0.008733, steps = 140 shifted from previous position = 28.8 rotated from previous position = 50.2 degrees atoms outside contour = 7787, contour level = 0.4641 Position of 5w1k (#1) relative to cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.66803839 0.13089917 -0.73252312 287.15892146 -0.00306040 -0.98391467 -0.17861290 133.48619549 -0.74412052 0.12156208 -0.65689217 103.92663988 Axis 0.91262340 0.03525963 -0.40727790 Axis point 0.00000000 52.33535540 121.73464757 Rotation angle (degrees) 170.53429629 Shift along axis 224.44760017 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.26183,-0.39834,-0.87907,177.93,0.63753,-0.75522,0.15233,-35.858,-0.72457,-0.52054,0.4517,152.54 > view matrix models > #3,-0.26183,-0.39834,-0.87907,168.97,0.63753,-0.75522,0.15233,-14.813,-0.72457,-0.52054,0.4517,137.84 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.49697,-0.48153,-0.72191,30.122,-0.025404,-0.83963,0.54256,45.333,-0.8674,-0.2513,-0.4295,262.71 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.49697,-0.48153,-0.72191,24.763,-0.025404,-0.83963,0.54256,54.057,-0.8674,-0.2513,-0.4295,257.24 > view matrix models > #3,0.49697,-0.48153,-0.72191,31.71,-0.025404,-0.83963,0.54256,53.043,-0.8674,-0.2513,-0.4295,261.12 > view matrix models > #3,0.49697,-0.48153,-0.72191,26.69,-0.025404,-0.83963,0.54256,65.752,-0.8674,-0.2513,-0.4295,258.11 > fitmap #1 inMap #3 Fit molecule 5w1k (#1) to map cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) using 7787 atoms average map value = 0.6428, steps = 100 shifted from previous position = 11.9 rotated from previous position = 28.9 degrees atoms outside contour = 2840, contour level = 0.4641 Position of 5w1k (#1) relative to cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.96106099 0.10672836 0.25489377 269.82197391 0.18113642 -0.93991137 -0.28940665 165.21166593 0.20868965 0.32430799 -0.92264454 152.70036082 Axis 0.98996915 0.07453081 0.12002596 Axis point 0.00000000 63.06237054 71.47106152 Rotation angle (degrees) 161.94278546 Shift along axis 297.75679800 > view matrix models > #3,0.49697,-0.48153,-0.72191,18.686,-0.025404,-0.83963,0.54256,61.279,-0.8674,-0.2513,-0.4295,253.67 > fitmap #1 inMap #3 Fit molecule 5w1k (#1) to map cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) using 7787 atoms average map value = 0.6429, steps = 104 shifted from previous position = 10.2 rotated from previous position = 0.463 degrees atoms outside contour = 2838, contour level = 0.4641 Position of 5w1k (#1) relative to cryosparc_P64_J902_class_00_00040_volume_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.95943424 0.11406066 0.25782959 269.79914230 0.18897732 -0.93883155 -0.28789388 166.03775511 0.20922119 0.32493919 -0.92230202 152.75094570 Axis 0.98954844 0.07848854 0.12096877 Axis point 0.00000000 62.96399151 71.32204480 Rotation angle (degrees) 161.96168679 Shift along axis 298.48947304 > select subtract #3 Nothing selected > open /Users/tgewering/Downloads/cryosparc_P64_J908_004_volume_map.mrc Opened cryosparc_P64_J908_004_volume_map.mrc as #4, grid size 226,226,226, pixel 1.32, shown at level 0.00845, step 1, values float32 > hide #!1 models > hide #!3 models > ui mousemode right zoom > view orient > volume #4 level 0.06252 > ui mousemode right ""map eraser"" > volume erase #4 center 151.49,157.23,152.55 radius 52.232 outside true Opened cryosparc_P64_J908_004_volume_map.mrc copy as #6, grid size 226,226,226, pixel 1.32, shown at step 1, values float32 > volume erase #6 center 169.23,124.16,65.982 radius 52.206 > volume erase #6 center 142.19,137.45,90.639 radius 26.252 > volume erase #6 center 152.94,158.68,82.337 radius 26.252 > volume erase #6 center 157.68,138.85,216.37 radius 26.252 > volume erase #6 center 173.26,129.89,211.01 radius 26.252 > volume erase #6 center 138.64,148.9,217.66 radius 26.252 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M2 Pro 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: Mac Model Identifier: Mac14,9 Model Number: MPHE3LL/A Chip: Unknown Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.80.7 OS Loader Version: 8419.80.7 Software: System Software Overview: System Version: macOS 13.2.1 (22D68) Kernel Version: Darwin 22.3.0 Time since boot: 1 minute Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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 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: 2022.9.26 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 pip: 23.0 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 Window Toolkit can't reproduce all ChimeraX