id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19709 Crash in swap_buffers waking from sleep on Mac, macOS 26.1 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.1-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 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 0x00000001f04d2080 (most recent call first): File ""/Applications/ChimeraX-1.11.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.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 122 in make_current File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 555 in make_current File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 584 in use_shared_context File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 146 in render File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 115 in _redraw File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 169 in update_graphics_now File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 153 in resizeEvent File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 61 in event File ""/Applications/ChimeraX-1.11.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.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.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, 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""\/usr\/lib\/system\/libxpc.dylib"", ""name"" : ""libxpc.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 8204988416, ""size"" : 22864, ""uuid"" : ""c7d67fae-9e56-3633-be9d-0a5de4a2f055"", ""path"" : ""\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Libraries\/libCoreVMClient.dylib"", ""name"" : ""libCoreVMClient.dylib"" }, { ""source"" : ""P"", ""arch"" : ""arm64e"", ""base"" : 8205082624, ""size"" : 10160, ""uuid"" : ""a8dbdbc6-b7f8-32ab-b467-08e6134015cf"", ""path"" : ""\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Libraries\/libCVMSPluginSupport.dylib"", ""name"" : ""libCVMSPluginSupport.dylib"" } ], ""sharedCache"" : { ""base"" : 6499254272, ""size"" : 5609635840, ""uuid"" : ""b69ff43c-dbfd-3fb1-b4fe-a8fe32ea1062"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%) Writable regions: Total=1.2G written=22.3M(2%) resident=1234K(0%) swapped_out=21.1M(2%) unallocated=1.2G(98%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 160K 8 ColorSync 208K 12 CoreAnimation 5264K 76 CoreGraphics 48K 3 CoreServices 320K 2 CoreUI image data 4416K 36 Foundation 48K 2 Kernel Alloc Once 32K 1 MALLOC 460.8M 108 MALLOC guard page 3200K 4 Mach message 64K 2 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 944K 59 Stack 211.5M 60 Stack Guard 56.0M 1 VM_ALLOCATE 189.8M 264 VM_ALLOCATE (reserved) 352.0M 1 reserved VM address space (unallocated) __AUTH 5878K 651 __AUTH_CONST 89.4M 1040 __CTF 824 1 __DATA 37.7M 1132 __DATA_CONST 59.3M 1179 __DATA_DIRTY 8814K 900 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __INFO_FILTER 8 1 __LINKEDIT 622.9M 135 __OBJC_RO 78.3M 1 __OBJC_RW 2567K 1 __TEXT 1.3G 1166 __TEXT (graphics) 201.0M 35 __TPRO_CONST 128K 2 dyld private memory 560K 7 mapped file 336.8M 62 page table in kernel 1234K 1 shared memory 3712K 28 =========== ======= ======= TOTAL 3.9G 6990 TOTAL, minus reserved VM space 3.6G 6990 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""6d37153324b3ccbcd2e4d3b70e8a724019228c49"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000010 }, { ""rolloutId"" : ""645eb1d0417dab722a215927"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/Paper_CAV1_JAK1_addon/FigureX_n.cxc > open > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/AF3/fold_jak1_865_1154_cav1_80_100/fold_jak1_865_1154_cav1_80_100_model_0.cif Chain information for fold_jak1_865_1154_cav1_80_100_model_0.cif #1 --- Chain | Description A | . B | . Computing secondary structure > open > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/AF3/fold_jak1_865_1154_cav1_80_100/fold_jak1_865_1154_cav1_80_100_model_1.cif Chain information for fold_jak1_865_1154_cav1_80_100_model_1.cif #2 --- Chain | Description A | . B | . > open > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/AF3/fold_jak1_865_1154_cav1_80_100/fold_jak1_865_1154_cav1_80_100_model_2.cif Chain information for fold_jak1_865_1154_cav1_80_100_model_2.cif #3 --- Chain | Description A | . B | . > open > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/AF3/fold_jak1_865_1154_cav1_80_100/fold_jak1_865_1154_cav1_80_100_model_3.cif Chain information for fold_jak1_865_1154_cav1_80_100_model_3.cif #4 --- Chain | Description A | . B | . > open > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/AF3/fold_jak1_865_1154_cav1_80_100/fold_jak1_865_1154_cav1_80_100_model_4.cif Chain information for fold_jak1_865_1154_cav1_80_100_model_4.cif #5 --- Chain | Description A | . B | . > renumber #1/A start 855 300 residues renumbered > renumber #2/A start 855 300 residues renumbered > renumber #3/A start 855 300 residues renumbered > renumber #4/A start 855 300 residues renumbered > renumber #5/A start 855 300 residues renumbered > renumber #1/B start 80 31 residues renumbered > renumber #2/B start 80 31 residues renumbered > renumber #3/B start 80 31 residues renumbered > renumber #4/B start 80 31 residues renumbered > renumber #5/B start 80 31 residues renumbered > mmaker #2/A to #1/A Computing secondary structure 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 fold_jak1_865_1154_cav1_80_100_model_0.cif, chain A (#1) with fold_jak1_865_1154_cav1_80_100_model_1.cif, chain A (#2), sequence alignment score = 1572 RMSD between 294 pruned atom pairs is 0.251 angstroms; (across all 300 pairs: 0.689) > mmaker #3/A to #1/A Computing secondary structure 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 fold_jak1_865_1154_cav1_80_100_model_0.cif, chain A (#1) with fold_jak1_865_1154_cav1_80_100_model_2.cif, chain A (#3), sequence alignment score = 1573.8 RMSD between 292 pruned atom pairs is 0.240 angstroms; (across all 300 pairs: 0.598) > mmaker #4/A to #1/A Computing secondary structure 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 fold_jak1_865_1154_cav1_80_100_model_0.cif, chain A (#1) with fold_jak1_865_1154_cav1_80_100_model_3.cif, chain A (#4), sequence alignment score = 1563 RMSD between 296 pruned atom pairs is 0.237 angstroms; (across all 300 pairs: 0.371) > mmaker #5/A to #1/A Computing secondary structure 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 fold_jak1_865_1154_cav1_80_100_model_0.cif, chain A (#1) with fold_jak1_865_1154_cav1_80_100_model_4.cif, chain A (#5), sequence alignment score = 1568.4 RMSD between 293 pruned atom pairs is 0.294 angstroms; (across all 300 pairs: 0.598) > graphics silhouettes true > lighting soft > color #1-5/A grey > color #1-5/B:90-98 lawn green executed FigureX_n.cxc > set bgColor white > ui tool show ""Side View"" > save > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/Paper_CAV1_JAK1_addon/FigXA.png > width 1152 height 831 supersample 3 > hide #2 models > hide #3 models > hide #4 models > hide #5 models > select #1-5/B:90,92,94,98 195 atoms, 190 bonds, 20 residues, 5 models selected > show sel & #1 atoms > style sel & #1 ball Changed 39 atom styles > show #2 models > hide #2 models > show #2 models > hide #2 models > show #4 models > show #5 models > select add #4 2834 atoms, 2894 bonds, 347 residues, 5 models selected > select add #3 5473 atoms, 5598 bonds, 674 residues, 5 models selected > select add #2 8112 atoms, 8302 bonds, 1001 residues, 5 models selected > select subtract #3 5434 atoms, 5560 bonds, 670 residues, 4 models selected > select subtract #2 2756 atoms, 2818 bonds, 339 residues, 3 models selected > select subtract #4 78 atoms, 76 bonds, 8 residues, 2 models selected > select add #5 2717 atoms, 2780 bonds, 335 residues, 2 models selected > show #3 models > show #2 models > show sel atoms > undo > select #1-5/B:90,92,94,98 195 atoms, 190 bonds, 20 residues, 5 models selected > show sel atoms > style sel ball Changed 195 atom styles > color sel byhetero > select #1-5/B:90,92,94,98 195 atoms, 190 bonds, 20 residues, 5 models selected > color sel byhetero > style sel stick Changed 195 atom styles > color sel byhetero > select #1-5/B:90,92,94,98 195 atoms, 190 bonds, 20 residues, 5 models selected > color sel byhetero > hide #2 models > hide #3 models > hide #4 models > hide #1 models > show #1 models > show #2 models > show #3 models > show #4 models > save > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/Paper_CAV1_JAK1_addon/FigXA2.png > width 1152 height 831 supersample 3 > save > /Users/pc126390/Integrative_Modelling/Projet_CAVEOLIN/Paper_CAV1_JAK1_addon/FigXA3.png > width 1152 height 831 supersample 3 > hide #2 models > hide #3 models > hide #4 models > hide #5 models > select #1-5/B:90,92,94,98 195 atoms, 190 bonds, 20 residues, 5 models selected > style sel & #1 ball Changed 39 atom styles > label (#1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select #1/B:90,92,94,98 39 atoms, 38 bonds, 4 residues, 1 model selected > select zone sel 4.5 #1/A residues true Selected 134 atoms > show sel atoms > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > select clear > select zone sel 4.5 #1/A residues true No atoms or surfaces specified > select #1/B:90,92,94,98 39 atoms, 38 bonds, 4 residues, 1 model selected > select zone sel 4.5 #1/A residues true Selected 134 atoms > color sel byhetero > style sel ball Changed 134 atom styles > hide sel cartoons > select clear > hbonds #!1 reveal true 2780 hydrogen bonds found > ~hbonds > ui mousemode right distance > distance #1/A:1054@O #1/B:98@NE1 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/A MET 1054 O and /B TRP 98 NE1: 2.904Å > distance #1/B:98@NE1 #1/A:1056@OG Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B TRP 98 NE1 and /A SER 1056 OG: 3.651Å > distance #1/B:94@CG2 #1/A:1053@CD2 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B VAL 94 CG2 and /A LEU 1053 CD2: 5.073Å > distance #1/B:94@CG2 #1/A:1101@CG2 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B VAL 94 CG2 and /A VAL 1101 CG2: 7.155Å > distance #1/B:94@CG2 #1/A:1045@CG1 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B VAL 94 CG2 and /A VAL 1045 CG1: 5.164Å > distance #1/B:94@CG2 #1/A:1048@CD2 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B VAL 94 CG2 and /A TYR 1048 CD2: 4.432Å > distance #1/B:92@CE2 #1/A:1046@CE1 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B PHE 92 CE2 and /A PHE 1046 CE1: 5.994Å > ui mousemode right translate > ui mousemode right distance > distance #1/A:1100@CG2 #1/B:92@CE2 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/A THR 1100 CG2 and /B PHE 92 CE2: 3.866Å > distance #1/B:92@CD1 #1/A:1101@CG2 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B PHE 92 CD1 and /A VAL 1101 CG2: 3.734Å > distance #1/B:92@CD2 #1/A:1045@CG2 Distance between fold_jak1_865_1154_cav1_80_100_model_0.cif #1/B PHE 92 CD2 and /A VAL 1045 CG2: 3.415Å ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 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 M4 Max OpenGL vendor: Apple Python: 3.11.9 Locale: fr_FR.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: Mac16,5 Model Number: Z1FV000H9FN/A Chip: Apple M4 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: 11 jours, 13 heures et 56 minutes Graphics/Displays: Apple M4 Max: Chipset Model: Apple M4 Max Type: GPU Bus: Built-In Total Number of Cores: 32 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 Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: LY0X41HPJ4 Display Firmware Version: Version 17.0 (Build 21A329) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 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 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: 2.7.11 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: 7.13.0 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: 4.25.1 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 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 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 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: 3.2.5 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 pytz: 2025.2 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: 4.0.0 roman-numerals-py: 4.0.0 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 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: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 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 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 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