id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19839 Crash saving session xukun.yuan@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-26.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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 0x00000001fff66080 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 52 in File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 61 in python_instances_of_class File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 2683 in File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py"", line 295 in File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/attributes.py"", line 295 in include_state File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 284 in discovery File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 741 in save File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 1058 in save File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/xky/Documents/Laboratory/Andy Sample From Europe/Aligned.cxs"" Opened cryosparc_P2_J137_008_volume_map.mrc as #1, grid size 384,384,384, pixel 0.76, shown at level 0.107, step 1, values float32 > view name session-start opened ChimeraX session > select /T:14 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 169 atoms, 172 bonds, 22 residues, 1 model selected > select up 241 atoms, 246 bonds, 30 residues, 1 model selected > delete sel > select clear > select /h:56 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 105 atoms, 107 bonds, 14 residues, 1 model selected > select up 494 atoms, 506 bonds, 63 residues, 1 model selected > delete sel > select clear > open ""/Users/xky/Documents/Laboratory/Andy Sample From > Europe/20250818/7n8o_PsbH.pdb"" Summary of feedback from opening /Users/xky/Documents/Laboratory/Andy Sample From Europe/20250818/7n8o_PsbH.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO b 4 LEU b 13 1 10 Start residue of secondary structure not found: HELIX 2 2 ASP b 15 PHE b 45 1 31 Start residue of secondary structure not found: HELIX 3 3 PRO b 54 GLN b 58 1 5 Start residue of secondary structure not found: HELIX 4 4 VAL b 62 LEU b 69 1 8 Start residue of secondary structure not found: HELIX 5 5 SER b 92 PHE b 117 1 26 27 messages similar to the above omitted Chain information for 7n8o_PsbH.pdb #2 --- Chain | Description h | No description available > select add #2 494 atoms, 506 bonds, 63 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,123.04,0,1,0,-86.203,0,0,1,9.2066 > view matrix models #2,1,0,0,115.09,0,1,0,-79.689,0,0,1,1.6685 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.44944,0.2758,-0.84967,111.47,0.61137,0.59854,0.51767,-30.885,0.65133,-0.75212,0.10039,206.26 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.44944,0.2758,-0.84967,95.917,0.61137,0.59854,0.51767,-28.744,0.65133,-0.75212,0.10039,184.15 > view matrix models > #2,0.44944,0.2758,-0.84967,107.86,0.61137,0.59854,0.51767,-15.783,0.65133,-0.75212,0.10039,182.54 > view matrix models > #2,0.44944,0.2758,-0.84967,107.25,0.61137,0.59854,0.51767,-22.279,0.65133,-0.75212,0.10039,179.97 > view matrix models > #2,0.44944,0.2758,-0.84967,115.07,0.61137,0.59854,0.51767,-22.166,0.65133,-0.75212,0.10039,174.24 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.67275,-0.36026,-0.64624,232.1,0.69503,0.60718,0.38505,-16.391,0.25367,-0.7082,0.65887,133.68 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.67275,-0.36026,-0.64624,231.5,0.69503,0.60718,0.38505,-14.448,0.25367,-0.7082,0.65887,134.82 > fitmap #2 inMap #1 Fit molecule 7n8o_PsbH.pdb (#2) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 494 atoms average map value = 0.06321, steps = 128 shifted from previous position = 3.15 rotated from previous position = 9.88 degrees atoms outside contour = 376, contour level = 0.10658 Position of 7n8o_PsbH.pdb (#2) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.73981381 0.47158635 -0.47987696 71.57750820 0.60478679 -0.15360397 0.78143382 116.23793291 0.29480251 -0.86833875 -0.39884753 337.97171929 Axis -0.90276672 -0.42390985 0.07288819 Axis point 0.00000000 165.27618562 143.66245269 Rotation angle (degrees) 113.97379854 Shift along axis -89.25805172 > view matrix models > #2,0.59896,-0.28486,-0.7484,222.43,0.6899,0.65804,0.30168,-18.706,0.40654,-0.69702,0.59067,136.07 > fitmap #2 inMap #1 Fit molecule 7n8o_PsbH.pdb (#2) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 494 atoms average map value = 0.06946, steps = 100 shifted from previous position = 2.25 rotated from previous position = 4.12 degrees atoms outside contour = 349, contour level = 0.10658 Position of 7n8o_PsbH.pdb (#2) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.76695091 0.46911198 -0.43785878 71.24955832 0.58206289 -0.22128916 0.78245381 130.71484400 0.27016505 -0.85496498 -0.44277058 342.65289959 Axis -0.91603279 -0.39609479 0.06318893 Axis point 0.00000000 167.38089505 142.48677565 Rotation angle (degrees) 116.65097390 Shift along axis -95.39053043 > view matrix models > #2,0.60335,-0.26475,-0.75225,217.99,0.70774,0.61249,0.35209,-12.722,0.36752,-0.74483,0.55692,148.19 > fitmap #2 inMap #1 Fit molecule 7n8o_PsbH.pdb (#2) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 494 atoms average map value = 0.06945, steps = 60 shifted from previous position = 2.36 rotated from previous position = 0.021 degrees atoms outside contour = 349, contour level = 0.10658 Position of 7n8o_PsbH.pdb (#2) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.76700463 0.46915498 -0.43771857 71.22915159 0.58205161 -0.22163423 0.78236452 130.78449128 0.27003679 -0.85485199 -0.44306688 342.65093529 Axis -0.91607084 -0.39600996 0.06316899 Axis point 0.00000000 167.37485698 142.47184907 Rotation angle (degrees) 116.66981151 Shift along axis -95.39799611 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.6123,0.12312,-0.78098,142.51,0.70559,0.36054,0.61004,23.337,0.35668,-0.92458,0.13389,211.09 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.6123,0.12312,-0.78098,142.32,0.70559,0.36054,0.61004,27.352,0.35668,-0.92458,0.13389,207.93 > fitmap #2 inMap #1 Fit molecule 7n8o_PsbH.pdb (#2) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 494 atoms average map value = 0.08299, steps = 148 shifted from previous position = 2.11 rotated from previous position = 18.6 degrees atoms outside contour = 307, contour level = 0.10658 Position of 7n8o_PsbH.pdb (#2) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.80257238 0.54402325 -0.24477814 47.38898592 0.49079683 -0.36890165 0.78932256 159.62604101 0.33911076 -0.75362480 -0.56307515 327.02792279 Axis -0.93478561 -0.35374566 -0.03224691 Axis point 0.00000000 162.09522626 128.77148262 Rotation angle (degrees) 124.38161384 Shift along axis -111.31120279 > view matrix models > #2,0.69327,-0.11511,-0.71142,186.11,0.64778,0.53216,0.54515,-4.5321,0.31584,-0.83878,0.4435,171.5 > ] Unknown command: ] > fitmap #2 inMap #1 Fit molecule 7n8o_PsbH.pdb (#2) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 494 atoms average map value = 0.08299, steps = 76 shifted from previous position = 2.09 rotated from previous position = 0.013 degrees atoms outside contour = 305, contour level = 0.10658 Position of 7n8o_PsbH.pdb (#2) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.80252336 0.54409810 -0.24477249 47.37344839 0.49076424 -0.36871937 0.78942799 159.57883183 0.33927391 -0.75365996 -0.56292978 327.02731557 Axis -0.93476284 -0.35380023 -0.03230828 Axis point 0.00000000 162.09178015 128.77678850 Rotation angle (degrees) 124.37194298 Shift along axis -111.30765562 > select clear > open ""/Users/xky/Documents/Laboratory/Andy Sample From > Europe/20250818/Cryosparc/J148_Nu-Refinement_3.06Å/Output.cif"" Summary of feedback from opening /Users/xky/Documents/Laboratory/Andy Sample From Europe/20250818/Cryosparc/J148_Nu-Refinement_3.06Å/Output.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for Output.cif #3 --- Chain | Description A | No description available B | No description available D | No description available E F P X | No description available I | No description available L | No description available M | No description available O | No description available S i | No description available a | No description available c | No description available f | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available > select #3/A 426 atoms, 457 bonds, 51 residues, 1 model selected > select ~sel & ##selected 4659 atoms, 5088 bonds, 602 residues, 1 model selected > delete sel > select add #3 426 atoms, 457 bonds, 51 residues, 1 model selected > view matrix models #3,1,0,0,-80.055,0,1,0,10.353,0,0,1,-54.289 > hide sel atoms > show sel cartoons Computing secondary structure > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.097553,0.19048,0.97683,-87.149,0.56498,0.79742,-0.21192,-23.534,-0.81932,0.57256,-0.029828,123.1 > view matrix models > #3,-0.029103,-0.14556,0.98892,-24.501,-0.18237,0.97351,0.13793,24.903,-0.9828,-0.17633,-0.054878,250.85 > view matrix models > #3,0.021667,-0.3917,0.91984,8.917,-0.42401,0.82961,0.36327,53.371,-0.9054,-0.39789,-0.14811,279.89 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.021667,-0.3917,0.91984,38.42,-0.42401,0.82961,0.36327,50.421,-0.9054,-0.39789,-0.14811,266.75 > view matrix models > #3,0.021667,-0.3917,0.91984,38.709,-0.42401,0.82961,0.36327,59.493,-0.9054,-0.39789,-0.14811,251.18 > view matrix models > #3,0.021667,-0.3917,0.91984,41.255,-0.42401,0.82961,0.36327,68.772,-0.9054,-0.39789,-0.14811,260.05 > view matrix models > #3,0.021667,-0.3917,0.91984,42.563,-0.42401,0.82961,0.36327,68.157,-0.9054,-0.39789,-0.14811,259.74 > fitmap #3 inMap #1 Fit molecule Output.cif (#3) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 426 atoms average map value = 0.07027, steps = 120 shifted from previous position = 1.8 rotated from previous position = 16 degrees atoms outside contour = 298, contour level = 0.10658 Position of Output.cif (#3) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.24959849 0.32584422 0.91188057 27.14755171 -0.93995888 0.14482629 -0.30903512 327.16876628 -0.23276159 -0.93426491 0.27013175 254.19693101 Axis -0.34400178 0.62978276 -0.69644558 Axis point 95.69552916 262.90535737 0.00000000 Rotation angle (degrees) 114.66551675 Shift along axis 19.67211449 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.60654,0.26198,0.75065,73.825,-0.71815,0.22457,-0.65865,322.06,-0.34113,-0.93858,0.051934,218.5 > fitmap #3 inMap #1 Fit molecule Output.cif (#3) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 426 atoms average map value = 0.06493, steps = 132 shifted from previous position = 2.73 rotated from previous position = 8.98 degrees atoms outside contour = 312, contour level = 0.10658 Position of Output.cif (#3) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.84984148 0.52458831 0.05076036 200.35217219 -0.50497483 -0.78290353 -0.36340409 387.80581284 -0.15089708 -0.33446856 0.93024776 80.53742467 Axis 0.02757012 0.19214158 -0.98097987 Axis point 157.30940811 172.84742450 0.00000000 Rotation angle (degrees) 148.34773571 Shift along axis 1.03176054 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.58634,0.24876,0.77093,68.853,-0.77947,0.085845,-0.62053,345.65,-0.22054,-0.96475,0.14356,191.99 > view matrix models > #3,-0.58634,0.24876,0.77093,68.569,-0.77947,0.085845,-0.62053,345.36,-0.22054,-0.96475,0.14356,196.7 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.68236,0.014133,0.73088,119.47,-0.71374,-0.22893,-0.66194,382.18,0.15797,-0.97334,0.1663,136.75 > fitmap #3 inMap #1 Fit molecule Output.cif (#3) to map cryosparc_P2_J137_008_volume_map.mrc (#1) using 426 atoms average map value = 0.1123, steps = 88 shifted from previous position = 3.57 rotated from previous position = 12 degrees atoms outside contour = 206, contour level = 0.10658 Position of Output.cif (#3) relative to cryosparc_P2_J137_008_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.98288450 0.05090401 -0.17705052 307.31773633 0.00079599 -0.95988401 -0.28039632 326.54078830 -0.18422127 -0.27573812 0.94341458 76.02848069 Axis 0.09163846 0.14106643 -0.98574979 Axis point 159.29863819 166.72876362 0.00000000 Rotation angle (degrees) 178.54360244 Shift along axis -0.71899419 > show sel atoms > style sel stick Changed 426 atom styles > hide sel atoms > select clear > save ""/Users/xky/Documents/Laboratory/Andy Sample From > Europe/20250818/aligned_PsbH_Psb35_CP47.cxs"" includeMaps true ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 Max OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,11 Model Number: MRW33CH/A Chip: Apple M3 Max Total Number of Cores: 14 (10 performance and 4 efficiency) Memory: 36 GB System Firmware Version: 13822.41.1 OS Loader Version: 13822.41.1 Software: System Software Overview: System Version: macOS 26.1 (25B78) Kernel Version: Darwin 25.1.0 Time since boot: 2 days, 22 hours, 32 minutes Graphics/Displays: Apple M3 Max: Chipset Model: Apple M3 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG UltraFine: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Sessions can't reproduce all ChimeraX