id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17774 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.7-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. 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""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6112d17137f5d11121dcd4e2"", ""factorPackIds"" : { }, ""deploymentId"" : 240000570 }, { ""rolloutId"" : ""62745b8e85854550ad70b6e4"", ""factorPackIds"" : { ""SIRI_TTS_DEVICE_TRAINING"" : ""6539d7f333b9b7499c6f1b63"" }, ""deploymentId"" : 240000073 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab with each protomer.cxs"" Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 1.1, shown at level 0.134, step 2, values float32 Log from Thu May 22 01:20:32 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab_glycan fitting.cxs"" Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 1.1, shown at level 0.12, step 2, values float32 Log from Wed May 21 18:28:54 2025UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab.cxs"" Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 1.1, shown at level 0.1, step 2, values float32 Log from Tue May 20 13:58:06 2025 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle > remotecontrol rest start port 55786 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 REST server started on host 127.0.0.1 port 55786 Visit http://127.0.0.1:55786/cmdline.html for CLI interface > open ""/Users/rk387/Documents/Experiments/Cryo-EM/Data > Processing/OPT_HIVenv_DH17-6/RealSpaceRefine_8/Unshielded HIV env OPT with > DH17_6 Fab_real_space_refined_006-coot-19_real_space_refined_008.pdb"" Chain information for Unshielded HIV env OPT with DH17_6 Fab_real_space_refined_006-coot-19_real_space_refined_008.pdb #1 --- Chain | Description A G | No description available B C | No description available D | No description available E | No description available H | No description available P | No description available > open ""/Users/rk387/Documents/Experiments/Cryo-EM/Data > Processing/OPT_HIVenv_DH17-6/cryosparc_P36_J75_006_volume_map_sharp.mrc"" Opened cryosparc_P36_J75_006_volume_map_sharp.mrc as #2, grid size 320,320,320, pixel 1.1, shown at level 0.0664, step 2, values float32 > surface dust #2 size 11 > hide atoms > show cartoons > set bgColor white > transparency 50 > volume #2 level 0.1 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab.cxs"" includeMaps true > select /B 995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected > select /P 1616 atoms, 1655 bonds, 211 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /P Alignment identifier is 1/P > color sel cyan > select /H 1750 atoms, 1800 bonds, 230 residues, 1 model selected > color sel blue > ui tool show ""Model Panel"" > color #1 #942193ff > color #1 #941751ff > color #1 #942193ff > color sel blue > select /P 1616 atoms, 1655 bonds, 211 residues, 1 model selected > color sel cyan > color zone #2 near sel & #1 distance 6.6 > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected > color zone #2 near sel & #1 distance 6.6 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.13 > volume #2 level 0.12 > color #2 #929292ff models > color #2 darkgrey models > color #2 silver models Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. [Repeated 1 time(s)] > color #1 darkgrey Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic models, 1 maps. [Repeated 2 time(s)] > transparency 50 > show #!1 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select /P 1616 atoms, 1655 bonds, 211 residues, 1 model selected > color sel cyan > select /H 1750 atoms, 1800 bonds, 230 residues, 1 model selected > color sel blue > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected > color zone #2 near sel & #1 distance 6.6 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.1 > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab.cxs"" includeMaps true ——— End of log from Tue May 20 13:58:06 2025 ——— opened ChimeraX session > transparency 0 > transparency 50 > ui tool show ""Model Panel"" > show #!1 models > select subtract #1 Nothing selected > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1991 atoms, 2066 bonds, 148 residues, 1 model selected > show sel atoms > color sel red > color zone #2 near sel & #1 distance 6.6 > transparency 0 > transparency 50 > volume #2 level 0.12 > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected > select subtract #1 Nothing selected > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > select /A 3938 atoms, 4049 bonds, 2 pseudobonds, 477 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A /G Alignment identifier is 1 > select /A,G:168 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A,G:168-171 80 atoms, 78 bonds, 8 residues, 1 model selected > select /A,G:167 16 atoms, 14 bonds, 2 residues, 1 model selected > select /A,G:167-177 210 atoms, 214 bonds, 22 residues, 1 model selected > select /A,G:172 18 atoms, 16 bonds, 2 residues, 1 model selected > select /A,G:172-177 114 atoms, 118 bonds, 12 residues, 1 model selected > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 2 models selected > select subtract #1 Nothing selected > movie record > turn y 2 180 > wait 180 > movie encode /Users/rk387/Desktop/movie1.mp4 Movie saved to /Users/rk387/Desktop/movie1.mp4 > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab_glycan fitting.cxs"" includeMaps true > hide #!2 models > show #!2 models > volume #2 level 0.2 > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > volume #2 level 0.12 > hide #!2 models > show #!2 models > hide #!1 models > volume #2 level 0.2027 [Repeated 1 time(s)] > show #!1 models > volume #2 level 0.1344 > volume #2 level 0.174 > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > volume #2 level 0.1056 > volume #2 level 0.12 > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > save /Users/rk387/Desktop/image1.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rk387/Desktop/movie2.mp4 Movie saved to /Users/rk387/Desktop/movie2.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rk387/Desktop/movie3.mp4 Movie saved to /Users/rk387/Desktop/movie3.mp4 > movie record > turn y 2 180 > wait 180 > movie encode /Users/rk387/Desktop/movie4.mp4 Movie saved to /Users/rk387/Desktop/movie4.mp4 > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab_glycan fitting.cxs"" includeMaps true ——— End of log from Wed May 21 18:28:54 2025 ——— opened ChimeraX session > volume #2 level 0.1584 > color zone #2 near #1 distance 6.6 > transparency 0 > transparency 50 > volume #2 level 0.134 > color zone #2 near #1 distance 6.6 > transparency 0 > transparency 50 > transparency 0 > ui tool show ""Model Panel"" > hide #!2 models > hide atoms > show surfaces [Repeated 1 time(s)] > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1991 atoms, 2066 bonds, 148 residues, 1 model selected > show sel surfaces > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 29 models selected > select subtract #1 35 models selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show cartoons > transparency #1.2-36 50 > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1991 atoms, 2066 bonds, 148 residues, 1 model selected > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1991 atoms, 2066 bonds, 148 residues, 1 model selected > show sel atoms > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 29 models selected > select subtract #1 35 models selected > transparency #1.2-36 0 > transparency #1.2-36 50 > transparency #1.2-36 0 > transparency #1.2-36 50 > transparency #1.2-36 0 > transparency #1.2-36 50 > show #!2 models > hide #!2 models > transparency #1.2-36 0 > lighting shadows false > lighting shadows true > lighting shadows false > select /C 995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected > select /A 3938 atoms, 4049 bonds, 2 pseudobonds, 477 residues, 2 models selected > color (#!1 & sel) light sea green > color (#!1 & sel) forest green > select /B 995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected > color (#!1 & sel) purple > select /C 995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected > color (#!1 & sel) forest green > select /E 952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected > color (#!1 & sel) gray > select /G 3949 atoms, 4063 bonds, 1 pseudobond, 478 residues, 2 models selected > color (#!1 & sel) purple > select /E 952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected > color (#!1 & sel) orange > select /H 1750 atoms, 1800 bonds, 230 residues, 1 model selected > select /G 3949 atoms, 4063 bonds, 1 pseudobond, 478 residues, 2 models selected > select /H 1750 atoms, 1800 bonds, 230 residues, 1 model selected > select /D 3950 atoms, 4062 bonds, 1 pseudobond, 477 residues, 2 models selected > color (#!1 & sel) orange > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 4 models selected > select subtract #1 35 models selected > select /A 3938 atoms, 4049 bonds, 2 pseudobonds, 477 residues, 2 models selected > color (#!1 & sel) light gray > select /B 995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected > color (#!1 & sel) dark gray > color (#!1 & sel) dim gray > color (#!1 & sel) gray > select /C 995 atoms, 1019 bonds, 1 pseudobond, 124 residues, 2 models selected > color (#!1 & sel) light gray > select /D 3950 atoms, 4062 bonds, 1 pseudobond, 477 residues, 2 models selected > color (#!1 & sel) light sea green > select /E 952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected > color (#!1 & sel) light sea green > select /E 952 atoms, 976 bonds, 1 pseudobond, 118 residues, 2 models selected > select /G 3949 atoms, 4063 bonds, 1 pseudobond, 478 residues, 2 models selected > color (#!1 & sel) dark gray > color (#!1 & sel) gray > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 4 models selected > select subtract #1 35 models selected > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1991 atoms, 2066 bonds, 148 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select /H 1750 atoms, 1800 bonds, 230 residues, 1 model selected > color (#!1 & sel) forest green > color (#!1 & sel) orange red > select /P 1616 atoms, 1655 bonds, 211 residues, 1 model selected > color (#!1 & sel) yellow > turn x +90 > turn x -90 [Repeated 1 time(s)] > turn x +90 > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 3 models selected > select subtract #1 35 models selected > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab with each protomer.cxs"" includeMaps true > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/OPT env DH17_6 fab with each protomer_top.tif"" width 840 height > 696 supersample 3 transparentBackground true > turn x +90 > turn x -90 [Repeated 1 time(s)] > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/OPT env DH17_6 fab with each protomer_side.tif"" width 840 height > 696 supersample 3 transparentBackground true > turn y -90 > turn y +90 [Repeated 1 time(s)] > turn y -90 > turn x -90 > turn x +90 [Repeated 1 time(s)] > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/OPT env DH17_6 fab with each protomer.cxs"" includeMaps true ——— End of log from Thu May 22 01:20:32 2025 ——— opened ChimeraX session > ui tool show ""Show Sequence Viewer"" > sequence chain /H Alignment identifier is 1/H > select /H:250 7 atoms, 6 bonds, 1 residue, 1 model selected > select /H:142-250 792 atoms, 813 bonds, 109 residues, 1 model selected > select /H:250 7 atoms, 6 bonds, 1 residue, 1 model selected > select /H:148-250 750 atoms, 769 bonds, 103 residues, 1 model selected > hide sel surfaces > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /P Alignment identifier is 1/P > select /P:231 4 atoms, 3 bonds, 1 residue, 1 model selected > select /P:121-231 854 atoms, 871 bonds, 111 residues, 1 model selected > select /P:231 4 atoms, 3 bonds, 1 residue, 1 model selected > select /P:127-231 805 atoms, 822 bonds, 105 residues, 1 model selected > select /P:129 7 atoms, 6 bonds, 1 residue, 1 model selected > select /P:129-231 787 atoms, 804 bonds, 103 residues, 1 model selected > select /P:127 11 atoms, 10 bonds, 1 residue, 1 model selected > select /P:127-231 805 atoms, 822 bonds, 105 residues, 1 model selected > hide sel surfaces > hide sel cartoons > turn x +90 > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/CE89_7_top.tif"" width 936 height 696 supersample 3 > transparentBackground true > turn x -90 > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/CE89_7_side.tif"" width 936 height 696 supersample 3 > transparentBackground true > lighting simple > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/CE89_7_side.tif"" width 936 height 696 supersample 3 > transparentBackground true > turn x +90 > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/CE89_7_top.tif"" width 936 height 696 supersample 3 > transparentBackground true > transparency sel 50 > transparency sel 0 > select /P:231 4 atoms, 3 bonds, 1 residue, 1 model selected > select /P:126-231 814 atoms, 831 bonds, 106 residues, 1 model selected > select /P:125 8 atoms, 7 bonds, 1 residue, 1 model selected > select /P:21-125 802 atoms, 823 bonds, 105 residues, 1 model selected > select /P:126 9 atoms, 8 bonds, 1 residue, 1 model selected > select /P:21-126 811 atoms, 832 bonds, 106 residues, 1 model selected > ui tool show ""Model Panel"" > select add #1 18975 atoms, 19540 bonds, 7 pseudobonds, 2303 residues, 3 models selected > transparency sel 50 > turn x 990 > turn x +90 > hide sel surfaces > turn x -90 > select subtract #1 35 models selected > turn x +90 > turn x -90 > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/CE89_7_side acrtoon.tif"" width 840 height 696 supersample 3 > transparentBackground true > turn x +90 > graphics silhouettes false > graphics silhouettes true > save ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/Images/CE89_7_top acrtoon.tif"" width 840 height 696 supersample 3 > transparentBackground true > open ""/Users/rk387/Documents/Experiments/Hahn Project/Presentation 05 23 > 2025/comparison of all natural Ab.cxs"" ===== 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 - 88.1 OpenGL renderer: Apple M3 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: MacBook Pro Model Identifier: Mac15,6 Model Number: MRX73LL/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 11881.1.1 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7 (23H124) Kernel Version: Darwin 23.6.0 Time since boot: 48 days, 23 hours, 20 minutes 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: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal T27i-30: 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 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 Core duplicate all ChimeraX