id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20255 Crash in QDockWidget::event() in Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 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 0x000000020281b100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, PIL._imaging, psutil._psutil_osx, psutil._psutil_posix, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, 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""logWritingSignature"" : ""cdb0278693b5d1159da4a4300f10915624fb9eab"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000044 }, { ""rolloutId"" : ""61675b89201f677a9a4cbd65"", ""factorPackIds"" : [ ""65a855f5f087695cfac03d1f"" ], ""deploymentId"" : 240000267 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > ui tool hide ""command line interface"" > ui tool show clix UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/wnicolas/Library/CloudStorage/OneDrive- > ExelixisInc/Documents/Phenix/KRAS_new_modalities/KRAS-LZTR1/E05593756.KRAS- > LZTR1/E05593756.KRAS-LZTR1-ISOLDE_1.pdb Chain information for E05593756.KRAS-LZTR1-ISOLDE_1.pdb #1 --- Chain | Description A | No description available B | No description available > open /Users/wnicolas/Library/CloudStorage/OneDrive- > ExelixisInc/Documents/Phenix/KRAS_new_modalities/KRAS-LZTR1/E05593756.KRAS- > LZTR1/cryosparc_P137_J131__localfilter.mrc Opened cryosparc_P137_J131__localfilter.mrc as #2, grid size 450,450,450, pixel 0.57, shown at level 4.26e-05, step 1, values float32 > volume #2 level 0.04261 > 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 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for E05593756.KRAS-LZTR1-ISOLDE_1.pdb #1.2 --- Chain | Description A | No description available B | No description available > clipper associate #2 toModel #1 Opened cryosparc_P137_J131__localfilter.mrc as #1.1.1.1, grid size 450,450,450, pixel 0.57, shown at step 1, values float32 > select clear > select up 79 atoms, 83 bonds, 1 residue, 1 model selected > isolde parameterise sel override true Loading residue template for XXX from internal database Running ANTECHAMBER command: /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/21/ydyj41hs15jdprk2zvztyh9h0000gp/T/tmp969gxwcs/ante.in.mol2 -fi mol2 -o /var/folders/21/ydyj41hs15jdprk2zvztyh9h0000gp/T/tmp969gxwcs/ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (XXX) `` (XXX) `Welcome to antechamber 20.0: molecular input file processor.` (XXX) `` (XXX) `Info: Finished reading file (/var/folders/21/ydyj41hs15jdprk2zvztyh9h0000gp/T/tmp969gxwcs/ante.in.mol2); atoms read (79), bonds read (83).` (XXX) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (XXX) `Running: /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (XXX) `` (XXX) `` (XXX) `Running: /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (XXX) `Info: Total number of electrons: 304; net charge: 1` (XXX) `` (XXX) `Running: /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (XXX) `` (XXX) `Running: /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (XXX) `` (XXX) `Running: /Applications/ChimeraX-1.11.1.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (XXX) `` Charges for residue XXX determined OpenMM ffXML file XXX written to the current working directory. New template added to forcefield as USER_XXX. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > select up 85 atoms, 87 bonds, 3 residues, 1 model selected > select up 7583 atoms, 7680 bonds, 480 residues, 1 model selected > isolde sim start /A-C ISOLDE: started sim > select clear > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > toolshed show > help phenix > ui tool show ""Water Placement"" Populating font family aliases took 54 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > phenix douse #1.1.1.1 nearModel #1.2 verbose true resolution 3 > volume #1.1.1.1 level 0.03722 Command: /Applications/phenix-1.21.1-5286/build/bin/phenix.douse map.mrc model.pdb resolution=3 stdout: Starting phenix.douse on Thu Apr 30 09:49:48 2026 by wnicolas =============================================================================== Processing files: ------------------------------------------------------------------------------- Found real_map, map.mrc Found model, model.pdb Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- resolution=3 Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = ""model.pdb"" } default_model = ""model.pdb"" real_map_files = ""map.mrc"" default_real_map = ""map.mrc"" } resolution = 3 Starting job =============================================================================== Removing water in input model number of water in input model to remove: 18 time (s): 0.090 (total time: 0.090) Process per chain (mode=per_chain) Working on chain A: Normalize and re-sample input map input map (min,max,mean): -0.236 0.351 0.000 re-scaled map (min,max,mean): 0.000 15.454 0.300 input map dimenstions: 86 91 84 input map grid steps (A): 0.570 0.570 0.570 re-sampled map dimenstions: 163 172 159 input map (min,max,mean): -0.660 15.996 0.301 time (s): 0.540 (total time: 0.630) Get cutoff mean density at atom centers: 2.327 density cutoff for peak search: 0.582 time (s): 0.100 (total time: 0.730) Mask out molecule/solvent regions time (s): 0.240 (total time: 0.970) Find peaks total peaks found: 1203 B factors set to : 30.485 time (s): 0.210 (total time: 1.180) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 1203 final: 61 time (s): 0.110 (total time: 1.290) Filter peaks by sphericity peaks left: 51 time (s): 0.350 (total time: 1.640) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 51 final: 50 time (s): 0.100 (total time: 1.740) Add to model and reset internals new water chain ID: 'A' time (s): 0.150 (total time: 1.890) Working on chain B: Normalize and re-sample input map input map (min,max,mean): -0.317 0.402 0.001 re-scaled map (min,max,mean): 0.000 17.564 0.272 input map dimenstions: 113 111 112 input map grid steps (A): 0.570 0.570 0.570 re-sampled map dimenstions: 214 210 212 input map (min,max,mean): -0.764 17.878 0.272 time (s): 1.090 (total time: 1.180) Get cutoff mean density at atom centers: 2.872 density cutoff for peak search: 0.718 time (s): 0.190 (total time: 1.370) Mask out molecule/solvent regions time (s): 0.400 (total time: 1.770) Find peaks total peaks found: 2295 B factors set to : 23.767 time (s): 0.380 (total time: 2.150) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 2295 final: 141 time (s): 0.200 (total time: 2.350) Filter peaks by sphericity peaks left: 121 time (s): 0.750 (total time: 3.100) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 121 final: 115 time (s): 0.190 (total time: 3.290) Add to model and reset internals new water chain ID: 'B' time (s): 0.280 (total time: 3.570) Working on chain C: Normalize and re-sample input map input map (min,max,mean): -0.236 0.351 0.005 re-scaled map (min,max,mean): 0.000 9.432 0.445 input map dimenstions: 46 38 37 input map grid steps (A): 0.570 0.570 0.570 re-sampled map dimenstions: 87 72 70 input map (min,max,mean): -0.461 9.670 0.444 time (s): 0.040 (total time: 0.130) Get cutoff mean density at atom centers: 2.266 density cutoff for peak search: 0.567 time (s): 0.000 (total time: 0.130) Mask out molecule/solvent regions time (s): 0.010 (total time: 0.140) Find peaks total peaks found: 102 B factors set to : 20.000 time (s): 0.010 (total time: 0.150) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 102 final: 3 time (s): 0.000 (total time: 0.150) Filter peaks by sphericity peaks left: 3 time (s): 0.020 (total time: 0.170) Filter peaks by distance distance (A), min: 2.00 max: 3.20 start: 3 final: 3 time (s): 0.000 (total time: 0.170) Add to model and reset internals new water chain ID: 'C' time (s): 0.010 (total time: 0.180) time (s): 10.980 (total time: 11.070) Attribute water to chains time (s): 0.510 (total time: 11.580) Summary Number of water added: 154 time (s): 0.020 (total time: 11.600) =============================================================================== Job complete usr+sys time: 22.32 seconds wall clock time: 22.50 seconds Placed 152 new waters in map ""cryosparc_P137_J131__localfilter.mrc"" near model ""E05593756.KRAS-LZTR1-ISOLDE_1.pdb"" Also, of the waters existing in the input, douse found 2 and did not find 4 > hbonds #2/A:1008-1049/B:1054-1159/C:1050-1053 interModel false reveal true > restrict any name ""Douse only water H-bonds"" 294 hydrogen bonds found > hbonds #2/B:1000/C:3 interModel false reveal true restrict any name ""In > common water H-bonds"" 4 hydrogen bonds found > hbonds #1.2/A:1006-1007/B:1003/C:2 interModel false reveal true restrict any > name ""Input only water H-bonds"" 6 hydrogen bonds found > select #2/A:1008-1049/B:1054-1159/C:1050-1053 152 atoms, 86 pseudobonds, 152 residues, 2 models selected > display #2/A:1008-1049/B:1054-1159/C:1050-1053 : view #2/A:1008-1049/B:1054-1159/C:1050-1053 @ Log: > ui tool hide ""command line interface"" > ui tool show clix UCSF ChimeraX version: 1.11.1 (2026-01-23) © 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 M2 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,5 Model Number: MPHG3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 Performance and 4 Efficiency) Memory: 32 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (a) (25D771280a) Kernel Version: Darwin 25.3.0 Time since boot: 1 day, 1 hour, 36 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 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: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL E2417H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported DELL E2417H: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 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: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 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-Clipper: 0.26.1 ChimeraX-clix: 0.2.6 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DAQplugin: 0.13.60 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: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ISOLDE: 1.11.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 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-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.5.4 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 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: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 flatbuffers: 25.12.19 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 mrcfile: 1.5.4 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 onnxruntime: 1.25.1 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 protobuf: 7.34.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 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 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit duplicate all ChimeraX