id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19793 Crash in QDockWidget::event croal939@… 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. 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All rights reserved. > open ""/Users/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/PCH45/PCH45 Modelling > Workspaces/PCH45_Gp63Beta_Feb_Finalizing.cxs"" Opened PCH45_Gp63Beta_Segmap_Jan.mrc as #6, grid size 416,416,204, pixel 1.37,1.37,1.37, shown at level 0.711, step 1, values float32 Log from Mon Feb 2 22:54:37 2026UCSF 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/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/Desktop/PCH45_Gp63Beta_1-90AAFit.pdb Chain information for PCH45_Gp63Beta_1-90AAFit.pdb #1 --- Chain | Description A | No description available > open ""/Users/croal939/Downloads/output_output (5).cif"" Summary of feedback from opening /Users/croal939/Downloads/output_output (5).cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for output_output (5).cif #2 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | No description available 9 | No description available A | No description available AA | No description available AB | No description available AC | No description available AD | No description available AE | No description available AF | No description available AG | No description available AH | No description available AI | No description available AJ | No description available AK | No description available AL | No description available AM | No description available AN | No description available AO | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available N | No description available O | No description available S | No description available X | No description available Z | No description available g | No description available j | No description available q | No description available > open ""/Users/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for > Distribution!/Gp63ing Pt.2/PCH45_Gp63b_Fitted1-coot-1.pdb"" Summary of feedback from opening /Users/croal939/Library/CloudStorage/OneDrive-UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for Distribution!/Gp63ing Pt.2/PCH45_Gp63b_Fitted1-coot-1.pdb --- warnings | End residue of secondary structure not found: HELIX 8 8 ALA A 171 GLU A 198 1 28 Start residue of secondary structure not found: HELIX 9 9 LEU A 199 LYS A 201 1 3 Chain information for PCH45_Gp63b_Fitted1-coot-1.pdb #3 --- Chain | Description A | No description available > open ""/Users/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for > Distribution!/Gp63ing Pt.2/63b_test2.mrc"" Opened 63b_test2.mrc as #4, grid size 416,416,416, pixel 1.37, shown at level 0.000262, step 2, values float32 > hide #2 models > show #2 models > select add #1 713 atoms, 730 bonds, 90 residues, 1 model selected > select subtract #1 Nothing selected > select add #4 2 models selected > open ""/Users/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for > Distribution!/Gp63ing Pt.2/PCH45_Gp63b_VZr4_Segmap1.mrc"" Opened PCH45_Gp63b_VZr4_Segmap1.mrc as #5, grid size 416,416,86, pixel 1.37,1.37,1.37, shown at level 0.000157, step 1, values float32 > open ""/Users/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/PCH45/PCH45 Modelling Workspaces/Gen 3 Models for > Distribution!/PCH45_Gp63Beta_Segmap_Jan.mrc"" Opened PCH45_Gp63Beta_Segmap_Jan.mrc as #6, grid size 416,416,204, pixel 1.37,1.37,1.37, shown at level 6.36e-05, step 2, values float32 > hide #!5 models > hide #!4 models > hide #3 models > color #2 #929292ff > hide #1-2 atoms > show #1-2 cartoons Computing secondary structure > set bgColor white > graphics silhouettes true > select add #6 4 models selected > volume #4 step 1 > show #!4 models > close #4 > show #!5 models > select add #5 4 models selected > close #5 > volume #6 step 1 > volume #6 level 0.711 > select clear > select add #2 2000 atoms, 1972 bonds, 250 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,22.818,0,1,0,-22.448,0,0,1,119.93 > view matrix models #2,1,0,0,0.25713,0,1,0,-0.55439,0,0,1,145.02 > select add #6 2000 atoms, 1972 bonds, 250 residues, 3 models selected > fitmap #2 inMap #6 Fit molecule output_output (5).cif (#2) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 2000 atoms average map value = 0.6873, steps = 48 shifted from previous position = 0.667 rotated from previous position = 0.128 degrees atoms outside contour = 1009, contour level = 0.71102 Position of output_output (5).cif (#2) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation 0.99999891 -0.00023246 -0.00146098 0.35866017 0.00023492 0.99999856 0.00168288 -0.40799733 0.00146059 -0.00168323 0.99999752 144.65036076 Axis -0.75109584 -0.65190410 0.10428850 Axis point 0.00000000 85010.15091267 -5526.98173801 Rotation angle (degrees) 0.12838840 Shift along axis 15.08195578 > transparency sel 50 > select clear > select add #1 713 atoms, 730 bonds, 90 residues, 1 model selected > view matrix models #1,1,0,0,-48.292,0,1,0,-26.491,0,0,1,229.92 > select add #6 713 atoms, 730 bonds, 90 residues, 3 models selected > surface dust #6 size 13.7 > select clear > select add #1 713 atoms, 730 bonds, 90 residues, 1 model selected > rainbow sel > select clear > select add #1 713 atoms, 730 bonds, 90 residues, 1 model selected > view matrix models #1,1,0,0,-91.309,0,1,0,-43.034,0,0,1,253.92 > view matrix models #1,1,0,0,-92.519,0,1,0,-39.23,0,0,1,240.64 > view matrix models #1,1,0,0,-95.536,0,1,0,-44.111,0,0,1,242.82 > select clear > select add #1 713 atoms, 730 bonds, 90 residues, 1 model selected > select add #6 713 atoms, 730 bonds, 90 residues, 3 models selected > fitmap #1 inMap #6 Fit molecule PCH45_Gp63Beta_1-90AAFit.pdb (#1) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 713 atoms average map value = 0.6914, steps = 60 shifted from previous position = 4.29 rotated from previous position = 0.0258 degrees atoms outside contour = 349, contour level = 0.71102 Position of PCH45_Gp63Beta_1-90AAFit.pdb (#1) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation 0.99999990 -0.00042223 -0.00012889 -97.79218147 0.00042222 0.99999991 -0.00008503 -44.93692375 0.00012893 0.00008498 0.99999999 239.25086380 Axis 0.18907213 -0.28673116 0.93916823 Axis point -42428.15039300 -329704.41775435 0.00000000 Rotation angle (degrees) 0.02575883 Shift along axis 219.09185132 > select clear > open > /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_0.cif Chain information for fold_pch45_gp63beta_91_end_model_0.cif #4 --- Chain | Description A | . > open > /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_1.cif Chain information for fold_pch45_gp63beta_91_end_model_1.cif #5 --- Chain | Description A | . > open > /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_2.cif Chain information for fold_pch45_gp63beta_91_end_model_2.cif #7 --- Chain | Description A | . > open > /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_3.cif Chain information for fold_pch45_gp63beta_91_end_model_3.cif #8 --- Chain | Description A | . > open > /Users/croal939/Downloads/fold_pch45_gp63beta_91_end/fold_pch45_gp63beta_91_end_model_4.cif Chain information for fold_pch45_gp63beta_91_end_model_4.cif #9 --- Chain | Description A | . Computing secondary structure [Repeated 4 time(s)] > ui tool show Matchmaker > matchmaker #4-5,7-9 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 output_output (5).cif, chain 2 (#2) with fold_pch45_gp63beta_91_end_model_0.cif, chain A (#4), sequence alignment score = 42.2 RMSD between 12 pruned atom pairs is 0.780 angstroms; (across all 28 pairs: 4.670) Matchmaker output_output (5).cif, chain 2 (#2) with fold_pch45_gp63beta_91_end_model_1.cif, chain A (#5), sequence alignment score = 42.2 RMSD between 13 pruned atom pairs is 1.191 angstroms; (across all 28 pairs: 3.647) Matchmaker output_output (5).cif, chain 2 (#2) with fold_pch45_gp63beta_91_end_model_2.cif, chain A (#7), sequence alignment score = 42.2 RMSD between 10 pruned atom pairs is 1.414 angstroms; (across all 28 pairs: 3.978) Matchmaker output_output (5).cif, chain 2 (#2) with fold_pch45_gp63beta_91_end_model_3.cif, chain A (#8), sequence alignment score = 42.2 RMSD between 11 pruned atom pairs is 1.177 angstroms; (across all 28 pairs: 3.973) Matchmaker output_output (5).cif, chain 2 (#2) with fold_pch45_gp63beta_91_end_model_4.cif, chain A (#9), sequence alignment score = 42.2 RMSD between 5 pruned atom pairs is 1.465 angstroms; (across all 28 pairs: 8.716) > hide #9 models > select add #6 2 models selected > select add #7 877 atoms, 890 bonds, 113 residues, 3 models selected > fitmap #7 inMap #6 Fit molecule fold_pch45_gp63beta_91_end_model_2.cif (#7) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms average map value = 0.5335, steps = 68 shifted from previous position = 1.44 rotated from previous position = 10.1 degrees atoms outside contour = 558, contour level = 0.71102 Position of fold_pch45_gp63beta_91_end_model_2.cif (#7) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation -0.86379141 0.30097549 -0.40407692 333.87967102 -0.35199663 -0.93429107 0.05655594 193.26113261 -0.36050350 0.19108625 0.91297496 351.44246211 Axis 0.20135982 -0.06521902 -0.97734370 Axis point 218.48834281 50.41390684 0.00000000 Rotation angle (degrees) 160.48494727 Shift along axis -288.85442718 > select subtract #7 2 models selected > select add #8 877 atoms, 890 bonds, 113 residues, 3 models selected > fitmap #8 inMap #6 Fit molecule fold_pch45_gp63beta_91_end_model_3.cif (#8) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms average map value = 0.5154, steps = 180 shifted from previous position = 1.14 rotated from previous position = 14 degrees atoms outside contour = 565, contour level = 0.71102 Position of fold_pch45_gp63beta_91_end_model_3.cif (#8) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation -0.37992807 -0.14267041 -0.91394738 335.20161826 -0.37136621 -0.88138741 0.29196467 195.41925835 -0.84719644 0.45033475 0.28188085 351.54518251 Axis 0.55359759 -0.23333425 -0.79942782 Axis point 296.62850733 27.82302033 0.00000000 Rotation angle (degrees) 171.77636703 Shift along axis -141.06619499 > select subtract #8 2 models selected > select add #5 877 atoms, 890 bonds, 113 residues, 3 models selected > fitmap #5 inMap #6 Fit molecule fold_pch45_gp63beta_91_end_model_1.cif (#5) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms average map value = 0.4988, steps = 96 shifted from previous position = 2.04 rotated from previous position = 13.4 degrees atoms outside contour = 581, contour level = 0.71102 Position of fold_pch45_gp63beta_91_end_model_1.cif (#5) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation 0.97610708 -0.20200812 -0.08004804 335.05559155 -0.14914265 -0.35494475 -0.92291424 195.46808550 0.15802354 0.91280170 -0.37659211 351.41021431 Axis 0.99129086 -0.12855921 0.02854748 Axis point 0.00000000 3.40483896 250.95847808 Rotation angle (degrees) 112.19220911 Shift along axis 317.04019826 > select clear > select add #7 877 atoms, 890 bonds, 113 residues, 1 model selected > select clear > select add #7 877 atoms, 890 bonds, 113 residues, 1 model selected > fitmap #7 inMap #6 Fit molecule fold_pch45_gp63beta_91_end_model_2.cif (#7) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms average map value = 0.5334, steps = 64 shifted from previous position = 0.0191 rotated from previous position = 0.0104 degrees atoms outside contour = 559, contour level = 0.71102 Position of fold_pch45_gp63beta_91_end_model_2.cif (#7) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation -0.86387301 0.30094938 -0.40392189 333.87142005 -0.35193005 -0.93431665 0.05654771 193.27643367 -0.36037295 0.19100229 0.91304406 351.44981825 Axis 0.20127884 -0.06519287 -0.97736212 Axis point 218.46861706 50.43487334 0.00000000 Rotation angle (degrees) 160.48821242 Shift along axis -288.89273304 > select add #6 877 atoms, 890 bonds, 113 residues, 3 models selected > fitmap #7 inMap #6 Fit molecule fold_pch45_gp63beta_91_end_model_2.cif (#7) to map PCH45_Gp63Beta_Segmap_Jan.mrc (#6) using 877 atoms average map value = 0.5334, steps = 40 shifted from previous position = 0.00155 rotated from previous position = 0.00256 degrees atoms outside contour = 558, contour level = 0.71102 Position of fold_pch45_gp63beta_91_end_model_2.cif (#7) relative to PCH45_Gp63Beta_Segmap_Jan.mrc (#6) coordinates: Matrix rotation and translation -0.86386400 0.30093943 -0.40394857 333.87213141 -0.35193807 -0.93431167 0.05657999 193.27513580 -0.36038672 0.19104229 0.91303026 351.45018069 Axis 0.20129025 -0.06521215 -0.97735849 Axis point 218.47066884 50.43021511 0.00000000 Rotation angle (degrees) 160.48819695 Shift along axis -288.89149822 > select clear > hide #1 models > show #1 models > hide #5 models > hide #4 models > hide #7 models > hide #8 models > show #7 models > select add #7 877 atoms, 890 bonds, 113 residues, 1 model selected > sequence chain #7/A Alignment identifier is 7/A > select clear > select add #1 713 atoms, 730 bonds, 90 residues, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > combine #1 #7 Remapping chain ID 'A' in fold_pch45_gp63beta_91_end_model_2.cif #7 to 'B' > select add #10 2303 atoms, 2350 bonds, 293 residues, 2 models selected > changechains #10 A,B,C A,A,A Proposed chain ID change would produce multiple residues with the samechain- ID/number/insertion-code combo (A/1/) > changechains chains #10 A,B,C A,A,A Expected ',' or a keyword > sequence chain #1/A#10/A Alignment identifier is 1 > sequence chain #10/B Alignment identifier is 10/B > changechains chains #10 1,B,C A,A,A Expected ',' or a keyword > changechains chains #10 A,B,C A,A,A Expected ',' or a keyword > changechains chains #10 A, B , C A,A,A Expected ',' or a keyword > sequence chain #1/A#10/A Alignment identifier is 1 > sequence chain #10/B Alignment identifier is 10/B > select clear > save ""/Users/croal939/Library/CloudStorage/OneDrive- > UniversityofOtago/PCH45/PCH45 Modelling > Workspaces/PCH45_Gp63Beta_Feb_Finalizing.cxs"" includeMaps true ——— End of log from Mon Feb 2 22:54:37 2026 ——— > view name session-start opened ChimeraX session 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 Pro Model Identifier: Mac15,3 Model Number: Z1C80004VX/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 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 hours, 45 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 XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal 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 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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 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