id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20237 Crash on Mac waking from sleep in OpenGL swap_buffers on status line expose event 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: Bus error Current thread 0x00000001fa427100 (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/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event 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, 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REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= .note.gnu.proper 320 1 Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 608K 18 ColorSync 160K 10 CoreAnimation 1632K 87 CoreGraphics 32K 2 CoreGraphics (reserved) 16K 1 reserved VM address space (unallocated) CoreUI image data 4192K 38 Foundation 48K 2 Kernel Alloc Once 32K 1 MALLOC 314.6M 88 MALLOC guard page 3392K 4 Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 56.6M 38 Stack 192.3M 38 VM_ALLOCATE 174.5M 225 VM_ALLOCATE (reserved) 160.0M 1 reserved VM address space (unallocated) __AUTH 5968K 655 __AUTH_CONST 90.2M 1041 __CTF 824 1 __DATA 42.4M 1126 __DATA_CONST 59.4M 1174 __DATA_DIRTY 8494K 898 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 618.1M 129 __OBJC_RO 78.4M 1 __OBJC_RW 2571K 1 __TEXT 1.5G 1195 __TEXT (graphics) 4832K 2 __TPRO_CONST 128K 2 dyld private memory 432K 4 mapped file 384.2M 69 page table in kernel 1122K 1 shared memory 3184K 25 =========== ======= ======= TOTAL 3.7G 6891 TOTAL, minus reserved VM space 3.5G 6891 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4279ba56e95d5b131bbe2f0e34f1b7615252abde"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63f9578e238e7b23a1f3030a"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : [ ""657ba0a39ec5da283662e9d2"" ], ""deploymentId"" : 240000042 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== 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/suxining/Downloads/5LEO_SH3b with ligand.cif"" Summary of feedback from opening /Users/suxining/Downloads/5LEO_SH3b with ligand.cif --- notes | Fetching CCD MPD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/MPD/MPD.cif Fetching CCD SO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif 5LEO_SH3b with ligand.cif title: Complex structure of lysostaphin SH3b domain with peptidoglycan fragment [more info...] Chain information for 5LEO_SH3b with ligand.cif #1 --- Chain | Description | UniProt A B | Lysostaphin | LSTP_STASI 401-493 G H | GLY-GLY-GLY-GLY-GLY | Non-standard residues in 5LEO_SH3b with ligand.cif #1 --- MPD — (4S)-2-methyl-2,4-pentanediol SO4 — sulfate ion 5LEO_SH3b with ligand.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 11 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 1827 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #1 models > show #1 models > show ligand > select ligand 88 atoms, 78 bonds, 18 residues, 1 model selected > open /Users/suxining/Downloads/5LEO.pdb1 Summary of feedback from opening /Users/suxining/Downloads/5LEO.pdb1 --- warnings | Start residue of secondary structure not found: SHEET 1 AA3 6 LYS B 403 THR B 404 0 Start residue of secondary structure not found: SHEET 2 AA3 6 LEU B 410 PRO B 420 -1 O TYR B 411 N LYS B 403 Start residue of secondary structure not found: SHEET 3 AA3 6 ILE B 447 GLN B 455 -1 O ILE B 447 N PHE B 418 Start residue of secondary structure not found: SHEET 4 AA3 6 HIS B 458 THR B 464 -1 O TRP B 460 N MET B 453 Start residue of secondary structure not found: SHEET 5 AA3 6 ARG B 470 ASN B 479 -1 O ILE B 471 N TYR B 463 8 messages similar to the above omitted 5LEO.pdb1 title: Complex structure of lysostaphin SH3B domain with peptidoglycan fragment [more info...] Chain information for 5LEO.pdb1 #2 --- Chain | Description A | No description available H | No description available Non-standard residues in 5LEO.pdb1 #2 --- MPD — (4S)-2-methyl-2,4-pentanediol SO4 — sulfate ion 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 903 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #1 models > select ligand 127 atoms, 113 bonds, 26 residues, 2 models selected > open /Users/suxining/Downloads/endolysin.pdb Chain information for endolysin.pdb #3 --- Chain | Description A | No description available > hide #3 models > show #3 models > hide #3 models > show #3 models > tile 2 models tiled > select add #1 1866 atoms, 1627 bonds, 477 residues, 2 models selected > select subtract #1 39 atoms, 35 bonds, 8 residues, 1 model selected > hide #2 models > show #2 models > hide #3 models > show #3 models > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 5LEO.pdb1, chain A (#2) with endolysin.pdb, chain A (#3), sequence alignment score = 317.9 RMSD between 92 pruned atom pairs is 0.656 angstroms; (across all 93 pairs: 0.776) Unsupported scale factor (0.000000) detected on Display1 > open /Users/suxining/Downloads/4OLS.cif Summary of feedback from opening /Users/suxining/Downloads/4OLS.cif --- notes | Fetching CCD FE from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FE/FE.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 4OLS.cif title: The amidase-2 domain of LysGH15 [more info...] Chain information for 4OLS.cif #4 --- Chain | Description | UniProt A B C D | Endolysin | D6QY02_9CAUD 165-403 Non-standard residues in 4OLS.cif #4 --- FE — Fe (III) ion MG — magnesium ion ZN — zinc ion 4OLS.cif mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly 24 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 5868 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #2 models > select add #2 903 atoms, 792 bonds, 228 residues, 1 model selected > select subtract #2 Nothing selected > hide #3 models > show #3 models > hide #!4 models > show #!4 models > open /Users/suxining/Downloads/4OLS.pdb1 Summary of feedback from opening /Users/suxining/Downloads/4OLS.pdb1 --- warnings | Start residue of secondary structure not found: HELIX 9 9 SER B 221 ALA B 230 1 10 Start residue of secondary structure not found: HELIX 10 10 GLY B 233 ALA B 238 1 6 Start residue of secondary structure not found: HELIX 11 11 SER B 273 PHE B 278 1 6 Start residue of secondary structure not found: HELIX 12 12 SER B 290 TRP B 312 1 23 Start residue of secondary structure not found: HELIX 13 13 LEU B 323 PHE B 327 5 5 37 messages similar to the above omitted Cannot find LINK/SSBOND residue HIS (214 ) Cannot find LINK/SSBOND residue HIS (324 ) Cannot find LINK/SSBOND residue CYS (332 ) Cannot find LINK/SSBOND residue ZN (501 ) Cannot find LINK/SSBOND residue HIS (214 ) 7 messages similar to the above omitted 4OLS.pdb1 title: The amidase-2 domain of LYSGH15 [more info...] Chain information for 4OLS.pdb1 #5 --- Chain | Description A | No description available Non-standard residues in 4OLS.pdb1 #5 --- ZN — zinc ion 6 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 1467 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #!5 models > ui tool show Matchmaker > matchmaker #!4 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker endolysin.pdb, chain A (#3) with 4OLS.cif, chain A (#4), sequence alignment score = 404.5 RMSD between 135 pruned atom pairs is 0.712 angstroms; (across all 173 pairs: 2.675) > hide #!4 models > show #!5 models > ui tool show Matchmaker > matchmaker #!5 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker endolysin.pdb, chain A (#3) with 4OLS.pdb1, chain A (#5), sequence alignment score = 404.5 RMSD between 135 pruned atom pairs is 0.712 angstroms; (across all 173 pairs: 2.675) Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) Window position QRect(0,0 100x30) outside any known screen, using primary screen OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. ===== Log before crash end ===== Log: 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/suxining/Downloads/6RK4.pdb1 6RK4.pdb1 title: Lysostaphin SH3B P4-G5 complex, synchrotron dataset [more info...] Chain information for 6RK4.pdb1 #1 --- Chain | Description A | No description available Non-standard residues in 6RK4.pdb1 #1 --- EDO — 1,2-ethanediol (ethylene glycol) K5T — (2~{R})-2-[[(2~{S})-2-[[(4~{R})-5-azanyl-4-[[(2~{S})-2-azanylpropanoyl]amino]-5-oxidanylidene- pentanoyl]amino]-6-[2-[2-[2-[2-(2-azanylethanoylamino)ethanoylamino]ethanoylamino]ethanoylamino]ethanoylamino]hexanoyl]amino]propanoic acid 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 813 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 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 Air Model Identifier: Mac15,12 Model Number: MXCR3CH/A Chip: Apple M3 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 16 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: 40 days, 13 hours, 46 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal U27N3R: 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 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-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-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-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-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 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 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 msgpack: 1.1.1 multidict: 6.7.0 narwhals: 2.20.0 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: 2.4.4 numpy: 1.26.4 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 plotly: 6.5.2 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 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 pyKVFinder: 0.9.0 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 tomlkit: 0.14.0 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 Graphics duplicate all ChimeraX