id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16997 Crash in Side View swap_buffers chimerax-bug-report@… Greg Couch "{{{ 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: Aborted Thread 0x000070000dc66000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x00007ff84e680b00 (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/graphics/opengl.py"", line 235 in swap_buffers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 497 in swap_buffers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 191 in draw File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py"", line 288 in render File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py"", line 113 in _redraw File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 138 in invoke File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 237 in _activate File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 206 in activate File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py"", line 382 in activate_trigger File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 89 in draw_new_frame File ""/Applications/ChimeraX-1.6.1.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-1.6.1.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 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(2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/ekamsingh/Downloads/cryosparc_P445_J88_006_volume_map.mrc > /Users/ekamsingh/Downloads/cryosparc_P445_J90_005_volume_map.mrc > /Users/ekamsingh/Downloads/model_C2_homorefine-coot-0.pdb > /Users/ekamsingh/Downloads/model_C2_homorefine.pdb > /Users/ekamsingh/Downloads/cryosparc_P445_J53_007_volume_map(2).mrc Opened cryosparc_P445_J88_006_volume_map.mrc as #1, grid size 384,384,384, pixel 0.919, shown at level 0.091, step 2, values float32 Opened cryosparc_P445_J90_005_volume_map.mrc as #2, grid size 384,384,384, pixel 0.919, shown at level 0.0974, step 2, values float32 model_C2_homorefine-coot-0.pdb title: Human proteasome 20S core particle [more info...] Chain information for model_C2_homorefine-coot-0.pdb #3 --- Chain | Description | UniProt A O | proteasome subunit α type-2 | PSA2_HUMAN 1-234 B P | proteasome subunit α type-4 | PSA4_HUMAN 1-261 C Q | proteasome subunit α type-7 | PSA7_HUMAN 1-248 D R | proteasome subunit α type-5 | PSA5_HUMAN 1-241 E S | proteasome subunit α type-1 | PSA1_HUMAN 1-263 F T | proteasome subunit α type-3 | PSA3_HUMAN 1-255 G U | proteasome subunit α type-6 | PSA6_HUMAN 1-246 H V | proteasome subunit β type-7 | PSB7_HUMAN 1-277 I W | proteasome subunit β type-3 | PSB3_HUMAN 1-205 J X | proteasome subunit β type-2 | PSB2_HUMAN 1-201 K Y | proteasome subunit β type-5 | PSB5_HUMAN 1-263 L Z | proteasome subunit β type-1 | PSB1_HUMAN 1-241 M a | proteasome subunit β type-4 | PSB4_HUMAN 1-264 N b | proteasome subunit β type-6 | PSB6_HUMAN 1-239 model_C2_homorefine.pdb title: Human proteasome 20S core particle [more info...] Chain information for model_C2_homorefine.pdb #4 --- Chain | Description | UniProt A O | proteasome subunit α type-2 | PSA2_HUMAN 1-234 B P | proteasome subunit α type-4 | PSA4_HUMAN 1-261 C Q | proteasome subunit α type-7 | PSA7_HUMAN 1-248 D R | proteasome subunit α type-5 | PSA5_HUMAN 1-241 E S | proteasome subunit α type-1 | PSA1_HUMAN 1-263 F T | proteasome subunit α type-3 | PSA3_HUMAN 1-255 G U | proteasome subunit α type-6 | PSA6_HUMAN 1-246 H V | proteasome subunit β type-7 | PSB7_HUMAN 1-277 I W | proteasome subunit β type-3 | PSB3_HUMAN 1-205 J X | proteasome subunit β type-2 | PSB2_HUMAN 1-201 K Y | proteasome subunit β type-5 | PSB5_HUMAN 1-263 L Z | proteasome subunit β type-1 | PSB1_HUMAN 1-241 M a | proteasome subunit β type-4 | PSB4_HUMAN 1-264 N b | proteasome subunit β type-6 | PSB6_HUMAN 1-239 Opened cryosparc_P445_J53_007_volume_map(2).mrc as #5, grid size 384,384,384, pixel 0.919, shown at level 0.0921, step 2, values float32 > close session > open /Users/ekamsingh/Downloads/cryosparc_P445_J85_005_volume_map.mrc > /Users/ekamsingh/Downloads/model_C2_homorefine-coot-0.pdb > /Users/ekamsingh/Downloads/cryosparc_P445_J90_005_volume_map.mrc > /Users/ekamsingh/Downloads/cryosparc_P445_J88_006_volume_map.mrc > /Users/ekamsingh/Downloads/cryosparc_P445_J81_volume_map.mrc Opened cryosparc_P445_J85_005_volume_map.mrc as #1, grid size 384,384,384, pixel 0.919, shown at level 0.104, step 2, values float32 model_C2_homorefine-coot-0.pdb title: Human proteasome 20S core particle [more info...] Chain information for model_C2_homorefine-coot-0.pdb #2 --- Chain | Description | UniProt A O | proteasome subunit α type-2 | PSA2_HUMAN 1-234 B P | proteasome subunit α type-4 | PSA4_HUMAN 1-261 C Q | proteasome subunit α type-7 | PSA7_HUMAN 1-248 D R | proteasome subunit α type-5 | PSA5_HUMAN 1-241 E S | proteasome subunit α type-1 | PSA1_HUMAN 1-263 F T | proteasome subunit α type-3 | PSA3_HUMAN 1-255 G U | proteasome subunit α type-6 | PSA6_HUMAN 1-246 H V | proteasome subunit β type-7 | PSB7_HUMAN 1-277 I W | proteasome subunit β type-3 | PSB3_HUMAN 1-205 J X | proteasome subunit β type-2 | PSB2_HUMAN 1-201 K Y | proteasome subunit β type-5 | PSB5_HUMAN 1-263 L Z | proteasome subunit β type-1 | PSB1_HUMAN 1-241 M a | proteasome subunit β type-4 | PSB4_HUMAN 1-264 N b | proteasome subunit β type-6 | PSB6_HUMAN 1-239 Opened cryosparc_P445_J90_005_volume_map.mrc as #3, grid size 384,384,384, pixel 0.919, shown at level 0.0974, step 2, values float32 Opened cryosparc_P445_J88_006_volume_map.mrc as #4, grid size 384,384,384, pixel 0.919, shown at level 0.091, step 2, values float32 Opened cryosparc_P445_J81_volume_map.mrc as #5, grid size 384,384,384, pixel 0.919, shown at level 0.0979, step 2, values float32 > hide atoms > show cartoons > volume #1 step 1 > volume #4 step 1 > volume #5 step 1 > volume #3 step 1 > ui tool show ""Fit in Map"" > fitmap #2 inMap #1 Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map cryosparc_P445_J85_005_volume_map.mrc (#1) using 47753 atoms average map value = 0.1303, steps = 48 shifted from previous position = 1.26 rotated from previous position = 0.0943 degrees atoms outside contour = 18047, contour level = 0.1045 Position of model_C2_homorefine-coot-0.pdb (#2) relative to cryosparc_P445_J85_005_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.99999920 -0.00100396 0.00077017 -0.11807453 0.00100315 0.99999894 0.00105239 -0.24410022 -0.00077122 -0.00105162 0.99999915 1.56388927 Axis -0.63930730 0.46835303 0.60986197 Axis point 0.00000000 956.02088776 640.07844797 Rotation angle (degrees) 0.09428272 Shift along axis 0.91491742 > fitmap #2 inMap #3 Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map cryosparc_P445_J90_005_volume_map.mrc (#3) using 47753 atoms average map value = 0.1217, steps = 40 shifted from previous position = 0.103 rotated from previous position = 0.0841 degrees atoms outside contour = 18864, contour level = 0.097413 Position of model_C2_homorefine-coot-0.pdb (#2) relative to cryosparc_P445_J90_005_volume_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999992 -0.00010184 -0.00037400 -0.08767818 0.00010217 0.99999962 0.00086783 -0.06799888 0.00037391 -0.00086787 0.99999955 1.22849693 Axis -0.91306520 -0.39343872 0.10732154 Axis point 0.00000000 1386.03759175 -29.23093170 Rotation angle (degrees) 0.05445840 Shift along axis 0.23865347 > fitmap #2 inMap #3 Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map cryosparc_P445_J90_005_volume_map.mrc (#3) using 47753 atoms average map value = 0.1217, steps = 40 shifted from previous position = 0.00588 rotated from previous position = 0.00664 degrees atoms outside contour = 18865, contour level = 0.097413 Position of model_C2_homorefine-coot-0.pdb (#2) relative to cryosparc_P445_J90_005_volume_map.mrc (#3) coordinates: Matrix rotation and translation 0.99999996 -0.00010787 -0.00026018 -0.11034384 0.00010809 0.99999964 0.00084711 -0.06362204 0.00026009 -0.00084714 0.99999961 1.24065131 Axis -0.94892380 -0.29140079 0.12095125 Axis point 0.00000000 1425.50997669 -18.29715026 Rotation angle (degrees) 0.05114906 Shift along axis 0.27330574 > fitmap #2 inMap #4 Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map cryosparc_P445_J88_006_volume_map.mrc (#4) using 47753 atoms average map value = 0.1119, steps = 44 shifted from previous position = 0.124 rotated from previous position = 0.105 degrees atoms outside contour = 19231, contour level = 0.091033 Position of model_C2_homorefine-coot-0.pdb (#2) relative to cryosparc_P445_J88_006_volume_map.mrc (#4) coordinates: Matrix rotation and translation 0.99999813 -0.00193278 -0.00009307 0.19822207 0.00193285 0.99999789 0.00069965 -0.35874598 0.00009172 -0.00069983 0.99999975 1.12174842 Axis -0.34006760 -0.04490483 0.93932826 Axis point 162.62154486 278.76797020 0.00000000 Rotation angle (degrees) 0.11789518 Shift along axis 1.00239052 > fitmap #2 inMap #5 Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map cryosparc_P445_J81_volume_map.mrc (#5) using 47753 atoms average map value = 0.1169, steps = 48 shifted from previous position = 1.86 rotated from previous position = 0.113 degrees atoms outside contour = 19413, contour level = 0.097901 Position of model_C2_homorefine-coot-0.pdb (#2) relative to cryosparc_P445_J81_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999902 -0.00067324 -0.00122848 0.17466824 0.00067532 0.99999833 0.00169711 -0.31273652 0.00122734 -0.00169793 0.99999781 -0.75976155 Axis -0.77128275 -0.55791034 0.30636410 Axis point 0.00000000 -412.95756728 247.31866665 Rotation angle (degrees) 0.12610273 Shift along axis -0.19300333 > fitmap #2 inMap #5 Fit molecule model_C2_homorefine-coot-0.pdb (#2) to map cryosparc_P445_J81_volume_map.mrc (#5) using 47753 atoms average map value = 0.1169, steps = 40 shifted from previous position = 0.0156 rotated from previous position = 0.00756 degrees atoms outside contour = 19386, contour level = 0.097901 Position of model_C2_homorefine-coot-0.pdb (#2) relative to cryosparc_P445_J81_volume_map.mrc (#5) coordinates: Matrix rotation and translation 0.99999884 -0.00069771 -0.00135614 0.20387953 0.00070004 0.99999828 0.00171924 -0.32214071 0.00135494 -0.00172019 0.99999760 -0.76292251 Axis -0.74817434 -0.58973610 0.30405014 Axis point 0.00000000 -409.48079695 253.68968434 Rotation angle (degrees) 0.13169739 Shift along axis -0.19452613 > set bgColor white > hide #!1 models > hide #!3 models > hide #!4 models > hide #!5 models > select /K/Y 3106 atoms, 3168 bonds, 402 residues, 1 model selected > color sel orange > select add #2 47753 atoms, 48594 bonds, 8 pseudobonds, 6152 residues, 2 models selected > select subtract #2 Nothing selected > select /H/V 3300 atoms, 3354 bonds, 438 residues, 1 model selected > color sel blue > select add #2 47753 atoms, 48594 bonds, 8 pseudobonds, 6152 residues, 2 models selected > select subtract #2 Nothing selected > select /J/X 3122 atoms, 3186 bonds, 392 residues, 1 model selected > color sel hot pink > show #!1 models > ui tool show ""Color Zone"" > color zone #1 near #2 distance 3.5 > color zone #3 near #2 distance 3.5 > color zone #4 near #2 distance 3.5 > show #!3 models > show #!4 models > show #!5 models > hide #!5 models > hide #!1 models > hide #!3 models > hide #!4 models > show #!5 models > color zone #5 near #2 distance 3.5 > ui tool show ""Side View"" > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > show #!1 models > show #!3 models > show #!4 models > color #1 white models ===== 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 INTEL-23.0.22 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 i7 Processor Speed: 2.8 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 8 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0) OS Loader Version: 582~3311 Software: System Software Overview: System Version: macOS 15.3.1 (24D70) Kernel Version: Darwin 24.3.0 Time since boot: 41 minutes, 9 seconds 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: No Connection Type: Internal MSI MP273A: 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: PB4H944500109 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 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-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-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 Graphics can't reproduce Tom Goddard all ChimeraX