id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16787 Crash moving window between screens chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000003f5df7000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001e85e4f40 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, 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crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/laschnei/Documents/KBTBD4/Models/250205_Sym_befIso.pdb Chain information for 250205_Sym_befIso.pdb #1 --- Chain | Description A B | No description available C D | No description available > open > /Users/laschnei/Documents/KBTBD4/Models/cryosparc_P2_J429_004_volume_map_sharp.mrc Opened cryosparc_P2_J429_004_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 1.08, shown at level 0.0684, step 1, values float32 > set bgColor white > volume #2 level 0.1094 > surface dust #2 size 10.8 > select #1 17100 atoms, 17410 bonds, 2180 residues, 1 model selected > show sel atoms > ui tool show ""Add Hydrogens"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > addh #1 Summary of feedback from adding hydrogens to 250205_Sym_befIso.pdb #1 --- notes | Termini for 250205_Sym_befIso.pdb (#1) chain A determined from SEQRES records Termini for 250205_Sym_befIso.pdb (#1) chain B determined from SEQRES records Termini for 250205_Sym_befIso.pdb (#1) chain C determined from SEQRES records Termini for 250205_Sym_befIso.pdb (#1) chain D determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /A SER 26, /B SER 26, /C SER 21, /D SER 21 Chain-final residues that are actual C termini: /A ALA 534, /B ALA 534, /C ALA 601, /D ALA 601 Chain-final residues that are not actual C termini: 2269 hydrogen bonds Adding 'H' to /A SER 26 Adding 'H' to /B SER 26 Adding 'H' to /C SER 21 Adding 'H' to /D SER 21 17182 hydrogens added > volume #2 color #b2b2b279 > ~select Nothing selected > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for 250205_Sym_befIso.pdb --- Chain | Description 1.2/A 1.2/B | No description available 1.2/C 1.2/D | No description available > clipper associate #2 toModel #1 Opened cryosparc_P2_J429_004_volume_map_sharp.mrc as #1.1.1.1, grid size 256,256,256, pixel 1.08, shown at step 1, values float32 > isolde sim start /A,C,B,D ISOLDE: started sim > ui tool show ""Ramachandran Plot"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 44 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > hide #1.3 models > show #1.3 models > hide #!1.2 models > show #!1.2 models > hide #!1.1 models > save /Users/laschnei/Documents/KBTBD4/Models/250205_Sym_afIso.pdb > open /Users/laschnei/Documents/KBTBD4/Models/250205_Sym_afIso.pdb Chain information for 250205_Sym_afIso.pdb #2 --- Chain | Description A B | No description available C D | No description available > open > /Users/laschnei/Documents/KBTBD4/Models/cryosparc_P2_J429_004_volume_map_sharp.mrc Opened cryosparc_P2_J429_004_volume_map_sharp.mrc as #3, grid size 256,256,256, pixel 1.08, shown at level 0.0684, step 1, values float32 > surface dust #3 size 10.8 > volume #3 level 0.08598 > hide #!1 models > hide #!1.2 models > hide #1.3 models > volume #3 color #ffffb284 > volume #3 color #ffffb285 > volume #3 level 0.1094 > open /Users/laschnei/Documents/KBTBD4/Models/250128_K4dim_PP2AAdim.pdb Chain information for 250128_K4dim_PP2AAdim.pdb #4 --- Chain | Description A B | No description available C D E F | No description available > hide #2,4 atoms > show #2,4 cartoons > hide #2 models > close #1.3#1#1.1-2 > hide #4 models > hide #!3 models > show #2 models > show #4 models > close #4 > color #2/A light cyan > color #2/A light blue > color #2/B steel blue > color #2/C hot pink > color #2/D light pink > show #!3 models > color zone #3 near #2 distance 5 > transparency #3 50 > save > /Users/laschnei/Documents/KBTBD4/Models/250205_K4dim_PAdim_improvedModel.cxs > includeMaps true > ui tool show ""Side View"" > volume #3 level 0.1153 > color zone #3 near #2 distance 5 > view #1 No objects specified. > view #2 > transparency #3 50 > show sel atoms > show #!3 models > open /Users/laschnei/Downloads/cryosparc_P2_J491_003_volume_map_sharp.mrc Opened cryosparc_P2_J491_003_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.08, shown at level 0.0715, step 1, values float32 > open /Users/laschnei/Downloads/cryosparc_P2_J491_003_volume_map_sharp.mrc Opened cryosparc_P2_J491_003_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.08, shown at level 0.0715, step 1, values float32 > surface dust #3 size 10.8 > surface dust #1 size 10.8 > surface dust #4 size 10.8 > close #4 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Fit in Map"" > fitmap #1 inMap #3 Fit map cryosparc_P2_J491_003_volume_map_sharp.mrc in map cryosparc_P2_J429_004_volume_map_sharp.mrc using 167634 points correlation = 0.3133, correlation about mean = 0.08974, overlap = 807.7 steps = 160, shift = 9.66, angle = 6 degrees Position of cryosparc_P2_J491_003_volume_map_sharp.mrc (#1) relative to cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.99979955 -0.01906381 0.00611867 9.48960351 0.01959116 0.99453158 -0.10258227 17.60071371 -0.00412961 0.10268158 0.99470570 -13.45091711 Axis 0.98154544 0.04900597 0.18484309 Axis point 0.00000000 153.07725452 159.74234359 Rotation angle (degrees) 6.00190696 Shift along axis 7.69070800 > fitmap #1 inMap #3 Fit map cryosparc_P2_J491_003_volume_map_sharp.mrc in map cryosparc_P2_J429_004_volume_map_sharp.mrc using 167634 points correlation = 0.3133, correlation about mean = 0.08972, overlap = 807.7 steps = 44, shift = 0.00324, angle = 0.00981 degrees Position of cryosparc_P2_J491_003_volume_map_sharp.mrc (#1) relative to cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.99980183 -0.01893677 0.00614054 9.46948138 0.01946657 0.99454551 -0.10247088 17.59799976 -0.00416658 0.10257011 0.99471705 -13.43197689 Axis 0.98171091 0.04934924 0.18387045 Axis point 0.00000000 152.98352373 159.88747298 Rotation angle (degrees) 5.99435241 Shift along axis 7.69499740 > select #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.9998,-0.018937,0.0061405,-10.6,0.019467,0.99455,-0.10247,42.093,-0.0041666,0.10257,0.99472,19.498 > view matrix models > #1,0.9998,-0.018937,0.0061405,-5.8056,0.019467,0.99455,-0.10247,18.443,-0.0041666,0.10257,0.99472,23.755 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.8647,0.14721,-0.48023,47.799,-0.31578,0.90284,-0.29184,100.01,0.39061,0.404,0.82717,-52.544 > view matrix models > #1,0.39958,0.44617,0.80079,-81.721,-0.91355,0.12147,0.38817,209.71,0.075919,-0.88667,0.45614,213.55 > view matrix models > #1,-0.66768,-0.70428,0.24124,291.46,-0.33188,-0.0084839,-0.94329,305.76,0.66638,-0.70987,-0.22807,188.93 > fitmap #1 inMap #3 Fit map cryosparc_P2_J491_003_volume_map_sharp.mrc in map cryosparc_P2_J429_004_volume_map_sharp.mrc using 167634 points correlation = 0.9136, correlation about mean = 0.6863, overlap = 4949 steps = 144, shift = 16.9, angle = 7.3 degrees Position of cryosparc_P2_J491_003_volume_map_sharp.mrc (#1) relative to cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.68390166 -0.71669623 0.13647352 306.45011025 -0.30796929 0.11401773 -0.94453950 295.47043720 0.66138750 -0.68800179 -0.29869735 209.46705236 Axis 0.35978805 -0.73617940 0.57322984 Axis point 200.12462599 0.00000000 257.55312466 Rotation angle (degrees) 159.11384359 Shift along axis 12.81060353 > ui mousemode right zoom > volume #1 level 0.0936 > ~select Nothing selected > volume #1 level 0.1618 > show #!3 models > hide #2 models The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear > show #2 models > hide #!1 models > show sel atoms > ui tool show ""Add Hydrogens"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select H 17182 atoms, 2180 residues, 1 model selected > hide sel atoms > ~select Nothing selected > show sel atoms > ~select Nothing selected > hide sel atoms > ~hbonds > select H 17182 atoms, 2180 residues, 1 model selected > delete atoms sel > delete bonds sel > show #!3 models > hide #!3 models > show #!1 models > view #1 > hide #!1 models > show sel atoms > ~select Nothing selected > volume #1 color #b2ffff80 > ~select Nothing selected > open /Users/laschnei/Downloads/cryosparc_P2_J493_003_volume_map_sharp.mrc Opened cryosparc_P2_J493_003_volume_map_sharp.mrc as #4, grid size 256,256,256, pixel 1.08, shown at level 0.0723, step 1, values float32 > select #4 4 models selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.38204,-0.83949,-0.3864,253.44,0.073121,0.44426,-0.89291,186.78,0.92125,0.31287,0.23111,-67.216 > view matrix models > #4,-0.60725,-0.40434,-0.68393,370.05,0.68182,0.17672,-0.70986,115.01,0.40789,-0.89737,0.16837,179.49 > view matrix models > #4,-0.67912,-0.23034,-0.69695,357.68,0.42658,0.64883,-0.63012,74.303,0.59734,-0.72523,-0.34237,198.18 > view matrix models > #4,-0.52274,-0.84683,-0.098098,340.76,-0.32249,0.30295,-0.89678,261.53,0.78914,-0.43715,-0.43146,143.82 > view matrix models > #4,-0.47982,-0.87102,-0.10537,339.15,-0.21069,0.23098,-0.94987,263.16,0.85169,-0.43357,-0.29434,116.24 > fitmap #4 inMap #3 Fit map cryosparc_P2_J493_003_volume_map_sharp.mrc in map cryosparc_P2_J429_004_volume_map_sharp.mrc using 167662 points correlation = 0.9135, correlation about mean = 0.6818, overlap = 4972 steps = 248, shift = 32.3, angle = 20.4 degrees Position of cryosparc_P2_J493_003_volume_map_sharp.mrc (#4) relative to cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.68562517 -0.71504712 0.13647620 306.44510486 -0.30763011 0.11468864 -0.94456881 295.45044861 0.65975893 -0.68960434 -0.29860344 209.94018074 Axis 0.35884860 -0.73649193 0.57341724 Axis point 199.94170787 0.00000000 257.61539199 Rotation angle (degrees) 159.19101567 Shift along axis 12.75384501 > ui mousemode right translate > ui mousemode right rotate > surface dust #4 size 10.8 > volume #4 level 0.1556 > hide #2 models > color zone #4 near #2 distance 4 > color zone #4 near #2 distance 3 > color zone #4 near #2 distance 3.5 > color zone #4 near #2 distance 4 > color zone #4 near #2 distance 4.5 > color zone #4 near #2 distance 6 > color zone #4 near #2 distance 4 > color zone #4 near #2 distance 3 > color zone #4 near #2 distance 4 > show #2 models > hide #!4 models > show sel atoms > show #!4 models > hide #!4 models > select clear > show sel atoms > select #2/C #2/D 9052 atoms, 9188 bonds, 1162 residues, 1 model selected > show sel atoms > color sel byhetero > ~sel] Unknown command: ~sel] > ~select Nothing selected > ui tool show Distances > distance /C:544@NE2 /D:76@OE2 Distance between /C GLN 544 NE2 and /D GLU 76 OE2: 4.638Å > distance /D:238@OE2 /C:588@NZ Distance between /D GLU 238 OE2 and /C LYS 588 NZ: 5.441Å > distance /D:277@OD2 /C:592@NE2 Distance between /D ASP 277 OD2 and /C GLN 592 NE2: 7.171Å > distance /D:273@OH /C:585@SD Distance between /D TYR 273 OH and /C MET 585 SD: 4.958Å > distance /C:589@OH /D:316@NE2 Distance between /C TYR 589 OH and /D HIS 316 NE2: 4.943Å > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > distance /D:589@OH /C:316@NE2 Distance between /D TYR 589 OH and /C HIS 316 NE2: 5.963Å > show #!4 models > hide #!5 models > hide #5.1 models > show #5.1 models > hide #!4 models > select clear > distance /C:76@OE2 /D:544@NE2 Distance between /C GLU 76 OE2 and /D GLN 544 NE2: 2.848Å > show #!4 models > hide #!4 models > show #!4 models > volume #4 color #937193 > volume #4 color #93719352 > distance /C:122@OE2 /D:578@NZ Distance between /C GLU 122 OE2 and /D LYS 578 NZ: 5.553Å > volume #4 level 0.1253 > hide #!4 models > distance /C:270@NH1 /D:585@SD Distance between /C ARG 270 NH1 and /D MET 585 SD: 5.185Å > show #!4 models > hide #!5 models > hide #5.1 models > hide #2 models > show #2 models > volume #4 color #d09fd0a1 > hide #!4 models > show #!5 models > show #5.1 models > ui tool show ""Side View"" ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/laschnei/Downloads/cryosparc_P2_J497_003_volume_map_sharp.mrc Opened cryosparc_P2_J497_003_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 1.08, shown at level 0.0794, step 1, values float32 OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AV000M7SM/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: 3 days, 2 hours, 37 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 DELL P2725H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 100.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.23.1 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX