id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19757 Crash in swap_buffers exposing status line during Mac wakeup, macOS 26.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.2-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 0x00000001f74bac40 (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/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, 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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""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_DMC1/transfer_11636725_files_2946497c/BRCA2map.cxs Opened cryosparc_P26_J759_009_volume_map.mrc as #1, grid size 336,336,336, pixel 0.745, shown at level 0.0137, step 2, values float32 Opened cryosparc_P26_J780_map_locres.mrc as #2, grid size 336,336,336, pixel 0.745, shown at level 6.08, step 2, values float32 > view name session-start opened ChimeraX session > select /A 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > volume #1 step 1 > volume #1 style mesh > graphics silhouettes false > select #1/X Nothing selected > select #1/X Nothing selected > show atoms > hide atoms > select #3/X 360 atoms, 395 bonds, 18 residues, 1 model selected > show sel atoms > style sel ball Changed 360 atom styles > select #3/E 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > rainbow sel > select #3/C 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > rainbow sel > select #3/X 360 atoms, 395 bonds, 18 residues, 1 model selected > sequence chain #3/X Alignment identifier is 3/X > select #3/O 66 atoms, 69 bonds, 8 residues, 1 model selected > show sel atoms > sequence chain #3/O Alignment identifier is 3/O > select #3/O 66 atoms, 69 bonds, 8 residues, 1 model selected > view sel > select zone sel 4.5 #1/C residues true No target atoms or surfaces > select zone sel 4.5 #3/C residues true Selected 99 atoms > show sel atoms > style sel ball Changed 99 atom styles > color sel bychain > color sel byhetero > hide sel cartoons > select #3/C 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > hide sel cartoons > show sel atoms > style sel ball Changed 2485 atom styles > color sel byhetero > show sel cartoons > view #3 clip false > select #3/C 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > color sel bychain > color sel byhetero > select #3 15583 atoms, 15863 bonds, 11 pseudobonds, 1971 residues, 3 models selected > color sel bychain > select #3/C 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > color sel byhetero > select #3/D 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > show sel atoms > style sel ball Changed 2485 atom styles > open 1V5W Summary of feedback from opening 1V5W fetched from pdb --- note | Fetching compressed mmCIF 1v5w from http://files.rcsb.org/download/1v5w.cif 1v5w title: Crystal structure of the human Dmc1 protein [more info...] Chain information for 1v5w #4 --- Chain | Description | UniProt A B | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 1-340 1v5w mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > hide #!3 models > view #4 clip false > open /Users/pc126390/Integrative_Modelling/Projet_DMC1/1V5W-assembly1.cif 1V5W-assembly1.cif title: Crystal structure of the human Dmc1 protein [more info...] Chain information for 1V5W-assembly1.cif #5 --- Chain | Description A A-2 A-3 A-4 B B-2 B-3 B-4 | Meiotic recombination protein DMC1/LIM15 homolog > hide #!4 models > hide #!5 atoms > show #!5 cartoons > open 8QQE Summary of feedback from opening 8QQE fetched from pdb --- note | Fetching compressed mmCIF 8qqe from http://files.rcsb.org/download/8qqe.cif 8qqe title: Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2 [more info...] Chain information for 8qqe #6 --- Chain | Description | UniProt A B | Meiotic recombination protein DMC1/LIM15 homolog | DMC1_HUMAN 2-340 C D | Breast cancer type 2 susceptibility protein | BRCA2_HUMAN 1398-1417 2398-2417 Non-standard residues in 8qqe #6 --- CL — chloride ion MG — magnesium ion 8qqe mmCIF Assemblies --- 1| author_defined_assembly 39 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 4377 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > close #6 > close #5 > close #4 > open /Users/pc126390/Integrative_Modelling/Projet_DMC1/8QQE-assembly1.cif 8QQE-assembly1.cif title: Crystal structure of the complex between DMC1 and the PhePP domain of BRCA2 [more info...] Chain information for 8QQE-assembly1.cif #4 --- Chain | Description A A-2 A-3 A-4 B B-2 B-3 B-4 | Meiotic recombination protein DMC1/LIM15 homolog C C-2 C-3 C-4 D D-2 D-3 D-4 | Breast cancer type 2 susceptibility protein Non-standard residues in 8QQE-assembly1.cif #4 --- CL — chloride ion MG — magnesium ion 156 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. 17508 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #!4 atoms > show #!4 cartoons > color #!4 bychain > mmaker #4/A to #3/C 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 BRCA2L-J759_m1_real_space_refined_001.pdb, chain C (#3) with 8QQE- assembly1.cif, chain A (#4), sequence alignment score = 1514.3 RMSD between 222 pruned atom pairs is 0.707 angstroms; (across all 296 pairs: 8.936) > view #3/C > show #!3 models > hide #!3 models > show #!3 models > view #4/D > select #4/D 39 atoms, 41 bonds, 5 residues, 1 model selected > show sel atoms > style sel ball Changed 39 atom styles > hide #!3 models > mmaker #4/B to #3/C 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 BRCA2L-J759_m1_real_space_refined_001.pdb, chain C (#3) with 8QQE- assembly1.cif, chain B (#4), sequence alignment score = 1453.7 RMSD between 222 pruned atom pairs is 0.703 angstroms; (across all 247 pairs: 2.555) > show #!3 models > view #4/B > hide #!3 models > show #!3 models > hide #!4 models > view #3/C > select #3/C 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > sequence chain #3/C Alignment identifier is 3/C > ui tool show ""Selection Inspector"" > select #3/X 360 atoms, 395 bonds, 18 residues, 1 model selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_structs.cxs > show #!1 models > show #!2 models > show #!4 models > hide #!1 models > hide #!2 models > hide #!4 models > select #3/A 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > select #3/A 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_A.pdb models #3 > selectedOnly true > select #3/B 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_B.pdb models #3 > selectedOnly true > select #3/C 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_C.pdb models #3 > selectedOnly true > select #3/D 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_D.pdb models #3 > selectedOnly true > select #3/E 2485 atoms, 2523 bonds, 2 pseudobonds, 319 residues, 3 models selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_E.pdb models #3 > selectedOnly true > select #3/F 2438 atoms, 2476 bonds, 1 pseudobond, 314 residues, 2 models selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_F.pdb models #3 > selectedOnly true > select #3/O 66 atoms, 69 bonds, 8 residues, 1 model selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/brca2_O.pdb models #3 > selectedOnly true > open /Users/pc126390/Integrative_Modelling/Projet_DMC1/brca2_O.pdb > /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_A.pdb > /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_B.pdb > /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_C.pdb > /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_D.pdb > /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_E.pdb > /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_F.pdb Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/brca2_O.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 151 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_A.pdb --- warnings | Start residue of secondary structure not found: HELIX 16 16 ILE B 24 HIS B 30 1 7 Start residue of secondary structure not found: HELIX 17 17 VAL B 34 VAL B 43 1 10 Start residue of secondary structure not found: HELIX 18 18 ILE B 48 MET B 53 1 6 Start residue of secondary structure not found: HELIX 19 19 ARG B 56 ASN B 61 1 6 Start residue of secondary structure not found: HELIX 20 20 GLU B 67 LEU B 80 1 14 125 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_B.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 125 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_C.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 125 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_D.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 125 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_E.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 124 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_F.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 126 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Chain information for brca2_O.pdb #5 --- Chain | Description O | No description available Chain information for dmc1_A.pdb #6 --- Chain | Description A | No description available Chain information for dmc1_B.pdb #7 --- Chain | Description B | No description available Chain information for dmc1_C.pdb #8 --- Chain | Description C | No description available Chain information for dmc1_D.pdb #9 --- Chain | Description D | No description available Chain information for dmc1_E.pdb #10 --- Chain | Description E | No description available Chain information for dmc1_F.pdb #11 --- Chain | Description F | No description available > hide #!3 models > hide #!6 models > show #!6 models > hide #5 models > show #5 models > hide #!6 models > show #!6 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > select #3/X 360 atoms, 395 bonds, 18 residues, 1 model selected > save /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_X.pdb models #3 > selectedOnly true > open /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_X.pdb Summary of feedback from opening /Users/pc126390/Integrative_Modelling/Projet_DMC1/dmc1_X.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE A 24 HIS A 30 1 7 Start residue of secondary structure not found: HELIX 2 2 VAL A 34 VAL A 43 1 10 Start residue of secondary structure not found: HELIX 3 3 ILE A 48 MET A 53 1 6 Start residue of secondary structure not found: HELIX 4 4 ARG A 56 ASN A 61 1 6 Start residue of secondary structure not found: HELIX 5 5 GLU A 67 LEU A 80 1 14 151 messages similar to the above omitted Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Cannot find LINK/SSBOND residue ANP (401 ) Chain information for dmc1_X.pdb #12 --- Chain | Description X | No description available Computing secondary structure > hide #5 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #12 models > show #!11 models > hide #!11 models > hide #!6 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > show #!9 models > show #!8 models > show #!7 models > show #!6 models > select #3/A:ANP 31 atoms, 33 bonds, 1 residue, 1 model selected > view sel No displayed objects specified. > select #3/A:ANP 31 atoms, 33 bonds, 1 residue, 1 model selected > view #8/A:ANP No objects specified. > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > show #12 models > hide #12 models > show #12 models > show #!4 models > hide #!4 models > show #!4 models > hide #!6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #12 models > show #!6 models > hide #!6 models > show #!6 models > show #!7 models Unsupported scale factor (0.000000) detected on Display0 ===== 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: 13822.61.10 OS Loader Version: 13822.61.10 Software: System Software Overview: System Version: macOS 26.2 (25C56) Kernel Version: Darwin 25.2.0 Time since boot: 2 jours, 12 heures et 55 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 Window Toolkit duplicate all ChimeraX