id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10034 Graphics crash, macOS 13.3.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 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 0x00007ff85ae90340 (most recent call first): File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 2730 in draw_elements File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1736 in draw File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 836 in _draw_geometry File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 771 in draw_self File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 764 in draw File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1551 in _draw_multiple File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1538 in draw_opaque File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py"", line 1563 in draw_depth File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 1438 in use_shadow_map File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 609 in _compute_shadowmaps File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 215 in _draw_scene File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 177 in draw File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 158 in update_graphics_now File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/graphics.py"", line 145 in resizeEvent File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/graphics.py"", line 57 in event File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 283 in event_loop File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 884 in init File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1035 in File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main 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\nmapped file 221.2M 58 \nshared memory 3172K 40 \n=========== ======= ======= \nTOTAL 2.7G 3369 \nTOTAL, minus reserved VM space 2.7G 3369 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""c225b0961fa7c5b0e10a9393376ebe663c17f89c"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""63508beab3714d3622fc7808"" }, ""deploymentId"" : 240000004 }, { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000338 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure > Files/Ab regions_GDIR_Glycans selected.cxs"" format session > set bgColor #ffffff00 opened ChimeraX session > select > /A,E-F:35-40,45-47,53-55,83-85,91-94,130-133,154-162,169-177,181-183,191-193,201-203,216-218,223-228,236-239,242-245,271-273,284-287,294-298,304-312,315-320,330-334,358-362,374-378,381-385,413-421,433-435,443-447,451-456,465-470,486-491,494-499 3780 atoms, 3801 bonds, 459 residues, 1 model selected > select /A,E-F:330 30 atoms, 30 bonds, 3 residues, 1 model selected > select /A,E-F:330 30 atoms, 30 bonds, 3 residues, 1 model selected > style sel stick Changed 30 atom styles > hide sel surfaces > color (#!1 & sel) red > color (#!1 & sel) orange > select CDRH1 204 atoms, 207 bonds, 27 residues, 1 model selected > select CDRH3 636 atoms, 663 bonds, 75 residues, 1 model selected > open /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta Failed opening file /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta: Sequence '7KDE_2|Chains D[auth E], E[auth F], F[auth G]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676)' differs in length from preceding sequences, and it is therefore impossible to open these sequences as an alignment. If you want to open the sequences individually, specify 'false' as the value of the 'alignment' keyword in the 'open' command. > open /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta Failed opening file /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta: Sequence '7KDE_2|Chains D[auth E], E[auth F], F[auth G]|Envelope glycoprotein gp120|Human immunodeficiency virus 1 (11676)' differs in length from preceding sequences, and it is therefore impossible to open these sequences as an alignment. If you want to open the sequences individually, specify 'false' as the value of the 'alignment' keyword in the 'open' command. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure > Files/Ab regions_GDIR_Glycans selected.cxs"" Log from Fri Aug 11 13:14:59 2023UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/kmckenney/Desktop/Infant bNAbs/EM/Original EM Files/High res > CP20.2_J198_C3_5_real_space_refined_012.pdb"" Chain information for High res CP20.2_J198_C3_5_real_space_refined_012.pdb #1 --- Chain | Description A E F | No description available B G I | No description available C J K | No description available D M N | No description available H O P | No description available L Q R | No description available > set bgColor white > select /E/F/B/G/I/C/J/K/D/M/N/O/P/Q/R 19512 atoms, 20022 bonds, 13 pseudobonds, 2475 residues, 2 models selected > hide sel atoms > select /A 3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected > select /H/L 1819 atoms, 1870 bonds, 240 residues, 1 model selected > style sel stick Changed 1819 atom styles > hide sel atoms > select /A 3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected > select /A 3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected > style sel stick Changed 3776 atom styles > ui mousemode right select Drag select of 584 atoms, 2 pseudobonds, 601 bonds > hide sel atoms Drag select of 7 atoms, 5 bonds > hide sel atoms Drag select of 384 atoms, 381 bonds > hide sel atoms Drag select of 136 atoms, 130 bonds > hide sel atoms Drag select of 416 atoms, 434 bonds > hide sel atoms Drag select of 2 atoms, 1 bonds > hide sel atoms Drag select of 1 atoms, 1 bonds > hide sel atoms Drag select of 11 atoms, 10 bonds > hide sel atoms Drag select of 11 atoms, 8 bonds > hide sel atoms Drag select of 5 atoms, 3 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms > select clear Drag select of 125 atoms, 134 bonds > name frozen N332 sel Drag select of 469 atoms, 1 pseudobonds, 474 bonds > hide sel atoms Drag select of 207 atoms, 209 bonds > hide sel atoms Drag select of 4 atoms, 3 bonds > hide sel atoms Drag select of 119 atoms, 109 bonds > hide sel atoms Drag select of 3 atoms, 3 bonds > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 1 atoms > hide sel atoms Drag select of 11 atoms, 8 bonds > hide sel atoms Drag select of 33 atoms, 34 bonds > name frozen N156 sel > select /A 3776 atoms, 3886 bonds, 6 pseudobonds, 459 residues, 3 models selected > show sel atoms > show sel surfaces > color (#!1 & sel) light gray > select clear > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > color (#!1 & sel) blue > select N156 33 atoms, 34 bonds, 3 residues, 1 model selected > color (#!1 & sel) blue > style sel stick Changed 33 atom styles > hide sel surfaces > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > hide sel surfaces > select /A:448@OD1 1 atom, 1 residue, 1 model selected > undo [Repeated 4 time(s)] > select /A 3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected > show sel surfaces > select /H/L 1819 atoms, 1870 bonds, 240 residues, 1 model selected > show sel atoms > ui tool show ""Show Sequence Viewer"" > sequence chain /A /E /F Alignment identifier is 1 > sequence chain /H /O /P Alignment identifier is 2 > sequence chain /L /Q /R Alignment identifier is 3 > select /H,O-P:1 27 atoms, 24 bonds, 3 residues, 1 model selected > select /H,O-P:1-26 534 atoms, 537 bonds, 78 residues, 1 model selected > select /H,O-P:1 27 atoms, 24 bonds, 3 residues, 1 model selected > select /H,O-P:1-25 522 atoms, 525 bonds, 75 residues, 1 model selected > name frozen FWR1-HC sel > select /H,O-P:26 12 atoms, 9 bonds, 3 residues, 1 model selected > select /H,O-P:26-34 204 atoms, 207 bonds, 27 residues, 1 model selected > name frozen CDRH1 sel > select /H,O-P:35 42 atoms, 45 bonds, 3 residues, 1 model selected > select /H,O-P:35-50 420 atoms, 438 bonds, 51 residues, 1 model selected > name frozen FWR2-HC sel > select /H,O-P:51 24 atoms, 21 bonds, 3 residues, 1 model selected > select /H,O-P:51-57 165 atoms, 168 bonds, 21 residues, 1 model selected > name frozen CDRH2 sel > select /H,O-P:58 33 atoms, 33 bonds, 3 residues, 1 model selected > select /H,O-P:58-92 918 atoms, 936 bonds, 114 residues, 1 model selected > name frozen FWR3-HC sel > select /H,O-P:93-94 48 atoms, 45 bonds, 6 residues, 1 model selected > select /H,O-P:93-102 636 atoms, 663 bonds, 75 residues, 1 model selected > name frozen CDRH3 sel > select /H,O-P:103 42 atoms, 45 bonds, 3 residues, 1 model selected > select /H,O-P:103-112 219 atoms, 222 bonds, 30 residues, 1 model selected > name frozen FWR4-HC sel > select /L,Q-R:3-4 45 atoms, 42 bonds, 6 residues, 1 model selected > select /L,Q-R:3-26 462 atoms, 468 bonds, 69 residues, 1 model selected > name frozen FWR1-LC sel > select /L,Q-R:27-27A 66 atoms, 63 bonds, 9 residues, 1 model selected > select /L,Q-R:27-32 162 atoms, 159 bonds, 24 residues, 1 model selected > name frozen CDRL1 sel > select /L,Q-R:33 21 atoms, 18 bonds, 3 residues, 1 model selected > select /L,Q-R:33-49 414 atoms, 429 bonds, 51 residues, 1 model selected > name frozen FWR2-LC sel > select /L,Q-R:50 18 atoms, 15 bonds, 3 residues, 1 model selected > select /L,Q-R:50-52 66 atoms, 63 bonds, 9 residues, 1 model selected > name frozen CDRL2 sel > select /L,Q-R:53-54 60 atoms, 57 bonds, 6 residues, 1 model selected > select /L,Q-R:53-88 783 atoms, 795 bonds, 108 residues, 1 model selected > name frozen FWR3-LC sel > select /L,Q-R:89-90 30 atoms, 27 bonds, 6 residues, 1 model selected > select /L,Q-R:89-97 279 atoms, 288 bonds, 36 residues, 1 model selected > name frozen CDRL3 sel > select /L,Q-R:98-99 45 atoms, 45 bonds, 6 residues, 1 model selected > select /L,Q-R:98-106A 207 atoms, 207 bonds, 30 residues, 1 model selected > name frozen FWR4-LC sel > select /A,E-F:324-325 36 atoms, 33 bonds, 6 residues, 1 model selected > select /A,E-F:324-327 93 atoms, 90 bonds, 12 residues, 1 model selected > name frozen GDIR sel > save ""/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure > Files/Ab regions_GDIR_Glycans selected.cxs"" > select /H 1028 atoms, 1060 bonds, 131 residues, 1 model selected > color sel magenta > show sel cartoons > hide sel atoms > select /L 791 atoms, 810 bonds, 109 residues, 1 model selected > show sel cartoons > hide sel atoms > select clear > select GDIR 3437 atoms, 90 bonds, 436 residues, 1 model selected > select N156 33 atoms, 34 bonds, 3 residues, 1 model selected > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > select CDRH3 636 atoms, 663 bonds, 75 residues, 1 model selected > select FWR3-LC 783 atoms, 795 bonds, 108 residues, 1 model selected > select FWR4-LC 207 atoms, 207 bonds, 30 residues, 1 model selected > select GDIR 3437 atoms, 90 bonds, 436 residues, 1 model selected > select /A,E-F:324 12 atoms, 9 bonds, 3 residues, 1 model selected > select /A,E-F:324-327 93 atoms, 90 bonds, 12 residues, 1 model selected > hide sel surfaces > name frozen GDIR_2 sel > select GDIR 3437 atoms, 90 bonds, 436 residues, 1 model selected > select GDIR_2 3437 atoms, 90 bonds, 436 residues, 1 model selected > select CDRL3 279 atoms, 288 bonds, 36 residues, 1 model selected > select clear > select /A,E-F:324 12 atoms, 9 bonds, 3 residues, 1 model selected > select /A,E-F:324-327 93 atoms, 90 bonds, 12 residues, 1 model selected > color (#!1 & sel) lime > show sel surfaces > hide sel surfaces > select /L 791 atoms, 810 bonds, 109 residues, 1 model selected > select /A 3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected > show sel surfaces > select clear > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > color (#!1 & sel) blue > show sel surfaces [Repeated 1 time(s)] > select clear [Repeated 1 time(s)] > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > show sel surfaces > select N156 33 atoms, 34 bonds, 3 residues, 1 model selected > show sel surfaces > hide sel atoms > show sel surfaces > show sel atoms > show sel cartoons > show sel surfaces > style sel sphere Changed 33 atom styles > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > style sel sphere Changed 125 atom styles > select clear > save ""/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure > Files/JPEG/V2 Figs/Fig 4b.jpg"" width 864 height 598 supersample 3 > select ::name=""BMA""::name=""MAN""::name=""NAG"" 1329 atoms, 1371 bonds, 102 residues, 1 model selected > style sel sphere Changed 1329 atom styles > select clear > save ""/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure > Files/JPEG/V2 Figs/Fig 4b.jpg"" width 864 height 598 supersample 3 > select N332 125 atoms, 134 bonds, 12 residues, 1 model selected > style sel stick Changed 125 atom styles > select /A,E-F:324 12 atoms, 9 bonds, 3 residues, 1 model selected > select /A,E-F:324-327 93 atoms, 90 bonds, 12 residues, 1 model selected > style sel stick Changed 93 atom styles > style sel stick Changed 93 atom styles > hide sel surfaces > show sel surfaces > hide sel surfaces > select N156 33 atoms, 34 bonds, 3 residues, 1 model selected > style sel stick Changed 33 atom styles > select CDRH3 636 atoms, 663 bonds, 75 residues, 1 model selected > show sel atoms > select clear > hide atoms > undo Drag select of 212 atoms > hide sel atoms [Repeated 1 time(s)]Drag select of 212 atoms > hide sel atoms > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,17.322,0,1,0,-36.04,0,0,1,-18.007 > view matrix models #1,1,0,0,25.96,0,1,0,-52.434,0,0,1,-28.503 > select /A,E-F:324-325 36 atoms, 33 bonds, 6 residues, 1 model selected > select /A,E-F:324-327 93 atoms, 90 bonds, 12 residues, 1 model selected > show sel atoms > save ""/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure > Files/Ab regions_GDIR_Glycans selected.cxs"" ——— End of log from Fri Aug 11 13:14:59 2023 ——— opened ChimeraX session OpenGL version: 4.1 INTEL-20.5.7 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.9.11 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: MacBookPro16,2 Processor Name: Quad-Core Intel Core i7 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0) OS Loader Version: 577~129 Software: System Software Overview: System Version: macOS 13.3.1 (a) (22E772610a) Kernel Version: Darwin 22.4.0 Time since boot: 14 days, 3 hours, 15 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal HP E27 G5: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: CNC3011BB8 Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 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-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 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: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 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: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX