id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19117 Crash in event loop vladimir.pelicic@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.7.6-x86_64-i386-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000700015cd3000 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700012c47000 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000700013ccd000 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000105003600 (most recent call first): File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, psutil._psutil_osx, psutil._psutil_posix, 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Bytes after previous region: 13592990994353 Bytes before following region: 91954421694544\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n CoreAnimation 153e7c000-153f5b000 [ 892K] rw-\/rwx SM=PRV \n---> GAP OF 0x5ffeac0a5000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV "", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x00000c5e315bffb0"",""rawCodes"":[1,13598694571952],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000c5e315bffb0""}, ""vmregioninfo"" : ""0xc5e315bffb0 is not in any region. 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""\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore"", ""name"" : ""QtWebEngineCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 140703511662592, ""CFBundleShortVersionString"" : ""6.9"", ""CFBundleIdentifier"" : ""com.apple.Foundation"", ""size"" : 3919872, ""uuid"" : ""61133096-d5f9-34bd-94b1-1e526ea018b1"", ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"", ""name"" : ""Foundation"", ""CFBundleVersion"" : ""1866"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4471779328, ""size"" : 66404352, ""uuid"" : ""7048d1fd-b9a9-3f6a-b752-ae8be69f6c3f"", ""path"" : ""\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" } ], ""sharedCache"" : { ""base"" : 140703492894720, ""size"" : 19331678208, ""uuid"" : ""246818c3-4b9f-3462-bcaf-fdf71975e5fe"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.1G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.1G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 2880K 4 \nCG image 6492K 38 \nColorSync 228K 27 \nCoreAnimation 12.7M 41 \nCoreGraphics 12K 2 \nCoreUI image data 2868K 21 \nFoundation 16K 1 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 333.3M 231 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 132K 33 \nStack 243.8M 34 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===== UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/vlad/Desktop/fig.cxs Log from Mon Oct 13 15:53:34 2025UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/vlad/Desktop/fig 4.cxs"" Log from Mon Oct 13 15:20:03 2025UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/vlad/Desktop/fig.cxs Log from Mon Oct 13 15:18:41 2025UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/vlad/Desktop/Fig. 1B .cxs"" Log from Fri Apr 4 10:51:11 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/Figures/Fig. 1/1B/Fig. 1B.cxs"" Log from Thu Apr 3 14:25:32 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/Figures/Fig. 1/1B/Fig. 1B.cxs"" Log from Thu Apr 3 12:55:30 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/Figures/Fig. 1/Fig. 1.cxs"" Log from Wed Apr 2 16:51:06 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/Vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/Figures/Fig. 1/Fig. 1.cxs"" Log from Wed Apr 2 12:58:16 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/Vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/Figures/Fig. 1/Fig. 1.cxs"" Log from Tue Apr 1 17:22:23 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/Figures/Fig. S2/s2.cxs"" Log from Thu Mar 27 17:19:06 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_pild/fold_pild_model_0.cif"" Chain information for fold_pild_model_0.cif #1 --- Chain | Description A | . Computing secondary structure Alignment identifier is 1/A > select /A:116 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:116 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > select /A:179 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:179 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > set bgColor white > lighting full [Repeated 1 time(s)] > graphics silhouettes true > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comc/fold_comc_model_0.cif"" Chain information for fold_comc_model_0.cif #2 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #2 to #1 Computing secondary structure [Repeated 1 time(s)] 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_pild_model_0.cif, chain A (#1) with fold_comc_model_0.cif, chain A (#2), sequence alignment score = 441.4 RMSD between 106 pruned atom pairs is 0.965 angstroms; (across all 217 pairs: 3.748) Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > select add #2 1758 atoms, 1797 bonds, 222 residues, 2 models selected Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A Alignment identifier is 2/A > select subtract #2 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1 1941 atoms, 1995 bonds, 247 residues, 1 model selected > select subtract #1 Nothing selected > select #2/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > select #2/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > style sel ball Changed 8 atom styles > select add #2 1750 atoms, 1790 bonds, 221 residues, 1 model selected > select subtract #2 Nothing selected > hide #2 models > show #2 models > hide #1 models > hide #2 models > show #1 models > view > save ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/comc/pild.cxs"" [Errno 20] Not a directory: '/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper Clément/Matos/comc' > save ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/s2.cxs"" ——— End of log from Thu Mar 27 17:19:06 2025 ——— opened ChimeraX session > show #2 models > hide #1 models > show #1 models > hide #2 models > view > save /Users/vlad/Desktop/image1.png supersample 3 > show #2 models > hide #1 models > save /Users/vlad/Desktop/image2.png supersample 3 > select #1/A:73 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:73-74 20 atoms, 20 bonds, 2 residues, 1 model selected > show #1 models > hide #2 models > select #1/A:101-102 11 atoms, 10 bonds, 2 residues, 1 model selected > select #1/A:101-102 11 atoms, 10 bonds, 2 residues, 1 model selected > hide #1 models > show #2 models > select #2/A:118 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:118-120 29 atoms, 30 bonds, 3 residues, 1 model selected > select #2/A:135-136 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:135-136 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/A:158-159 19 atoms, 19 bonds, 2 residues, 1 model selected > select #2/A:158-159 19 atoms, 19 bonds, 2 residues, 1 model selected > show #1 models > select add #2 1750 atoms, 1790 bonds, 221 residues, 1 model selected > select subtract #2 Nothing selected > view > undo > hide #2 models > show #2 models > save /Users/vlad/Desktop/image3.png supersample 3 > hide #1 models > hide #2 models > show #1 models > view orient [Repeated 1 time(s)] > undo [Repeated 3 time(s)] > show #1 models > hide #2 models > undo > rotate y, 90 Unknown command: rotate y, 90 > rotate Unknown command: rotate > turn y -90 [Repeated 3 time(s)] > turn x -90 > hide #2 models > select #1/A:179@OD1 1 atom, 1 residue, 1 model selected > view > show #2 models > hide #2 models > save /Users/vlad/Desktop/image4.png supersample 3 > hide #1 models > show #2 models > save /Users/vlad/Desktop/image5.png supersample 3 > save /Users/vlad/Desktop/image6.png supersample 3 > save /Users/vlad/Desktop/image7.png supersample 3 > save /Users/vlad/Desktop/S2.cxs ——— End of log from Tue Apr 1 17:22:23 2025 ——— opened ChimeraX session > hide #2 models > show #1 models > close #1 > rename #2 ComC > show #2 models > open ""/Users/Vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comc_comgc/fold_comc_comgc_model_0.cif"" Summary of feedback from opening /Users/Vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper Clément/Matos/AF3/fold_comc_comgc/fold_comc_comgc_model_0.cif --- note | Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif Chain information for fold_comc_comgc_model_0.cif #1 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/Vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comgc/fold_comgc_model_0.cif"" Chain information for fold_comgc_model_0.cif #3 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #1 to #2 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 ComC, chain A (#2) with fold_comc_comgc_model_0.cif, chain A (#1), sequence alignment score = 1124.7 RMSD between 211 pruned atom pairs is 0.740 angstroms; (across all 220 pairs: 0.929) > ui tool show Matchmaker > matchmaker #3 to #1 Computing secondary structure [Repeated 1 time(s)] 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_comc_comgc_model_0.cif, chain B (#1) with fold_comgc_model_0.cif, chain A (#3), sequence alignment score = 495.5 RMSD between 83 pruned atom pairs is 0.548 angstroms; (across all 105 pairs: 10.458) > rename #1 ComC/ComGC > rename #3 ComGC > save ""/Users/Vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comgc/Fig. 1.cxs"" ——— End of log from Wed Apr 2 12:58:16 2025 ——— opened ChimeraX session > hide #3 models > show #3 models > hide #1 models > color #1 #93cde9ff > hide #3 models > select add #2 1750 atoms, 1790 bonds, 221 residues, 1 model selected > hide #2 models > hide target m > show #1 models > select add #1 4304 atoms, 4391 bonds, 547 residues, 2 models selected > select subtract #2 2554 atoms, 2601 bonds, 326 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > show #2 models > select add #2 1750 atoms, 1790 bonds, 221 residues, 1 model selected > close #2 > show #1 models Alignment identifier is 1/A Alignment identifier is 1 > select #1/A:36 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:36 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:38-39 11 atoms, 10 bonds, 2 residues, 1 model selected > select #1/A:38-39 11 atoms, 10 bonds, 2 residues, 1 model selected > select #1/A:39 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:39 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:38 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:38 5 atoms, 4 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:61 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:61 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:64 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:64-65 10 atoms, 9 bonds, 2 residues, 1 model selected > select #1/A:64-65 10 atoms, 9 bonds, 2 residues, 1 model selected > select #1/A:64-65 10 atoms, 9 bonds, 2 residues, 1 model selected > hide sel atoms > select > #1/A:2-23,45-47,52-56,70-87,93-112,117-131,135-149,156-167,171-191,201-219 1190 atoms, 1209 bonds, 150 residues, 1 model selected > select #1/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:109 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > color sel byhetero > select > #1/A:2-23,45-47,52-56,70-87,93-112,117-131,135-149,156-167,171-191,201-219 1190 atoms, 1209 bonds, 150 residues, 1 model selected > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:158-159 19 atoms, 19 bonds, 2 residues, 1 model selected > select > #1/A:2-23,45-47,52-56,70-87,93-112,117-131,135-149,156-167,171-191,201-219 1190 atoms, 1209 bonds, 150 residues, 1 model selected > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:158-159 19 atoms, 19 bonds, 2 residues, 1 model selected > select > #1/A:2-23,45-47,52-56,70-87,93-112,117-131,135-149,156-167,171-191,201-219 1190 atoms, 1209 bonds, 150 residues, 1 model selected > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:158-159 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:158-159 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:158 8 atoms, 7 bonds, 1 residue, 1 model selected > style sel ball Changed 8 atom styles > show sel atoms > color sel byhetero > save ""/Users/Vlad/Desktop/Fig. 1.cxs"" > select #1/B:1 #3/A:1 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/B #3/A 1608 atoms, 1622 bonds, 210 residues, 2 models selected . [ID: 1] region chains A,B [1-105] RMSD: 10.458 > ui tool show ""Color Actions"" > color sel byelement > color sel bychain > color #3 #f3a39eff > show #3 models > select add #1 3358 atoms, 3412 bonds, 431 residues, 2 models selected > select subtract #3 2554 atoms, 2601 bonds, 326 residues, 1 model selected > select subtract #1 Nothing selected > hide #3 models > hide #1 models > show #3 models > show #1 models > save ""/Users/Vlad/Desktop/Fig. 1.cxs"" > view > turn x 90 > hide #3 models > rename #3 id #2 > save ""/Users/Vlad/Desktop/Fig. 1.cxs"" ——— End of log from Wed Apr 2 16:51:06 2025 ——— opened ChimeraX session > turn x -90 > select #1/B:1 #2/A:1 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/B:1-11 #2/A:1-11 174 atoms, 172 bonds, 22 residues, 2 models selected . [ID: 1] region chains A,B [1-11] RMSD: 31.931 > ui tool show ""Color Actions"" > color sel gold > select Zn 1 atom, 1 residue, 1 model selected > color sel black > save /Users/vlad/Desktop/image1.png supersample 3 > view > save /Users/vlad/Desktop/image2.png supersample 3 > save /Users/vlad/Desktop/1A.cxs ——— End of log from Thu Apr 3 12:55:30 2025 ——— opened ChimeraX session > close #2 > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comc_comgd/fold_comc_comgd_model_0.cif"" Chain information for fold_comc_comgd_model_0.cif #2 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comc_comge/fold_comc_comge_model_0.cif"" Chain information for fold_comc_comge_model_0.cif #3 --- Chain | Description A | . B | . Computing secondary structure > open ""/Users/vlad/Documents/My stuff/Science/3. Papers/5. Marseille/5. Paper > Clément/Matos/AF3/fold_comc_comgf/fold_comc_comgf_model_0.cif"" Chain information for fold_comc_comgf_model_0.cif #4 --- Chain | Description A | . B | . Computing secondary structure > ui tool show Matchmaker > matchmaker #2-4 to #1 Computing secondary structure [Repeated 2 time(s)] 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 ComC/ComGC, chain A (#1) with fold_comc_comgd_model_0.cif, chain A (#2), sequence alignment score = 1136.1 RMSD between 220 pruned atom pairs is 0.505 angstroms; (across all 220 pairs: 0.505) Matchmaker ComC/ComGC, chain A (#1) with fold_comc_comge_model_0.cif, chain A (#3), sequence alignment score = 1136.1 RMSD between 220 pruned atom pairs is 0.348 angstroms; (across all 220 pairs: 0.348) Matchmaker ComC/ComGC, chain A (#1) with fold_comc_comgf_model_0.cif, chain A (#4), sequence alignment score = 1136.1 RMSD between 220 pruned atom pairs is 0.400 angstroms; (across all 220 pairs: 0.400) > rename #2 ComC/ComGD > rename #3 ComC/ComGE > rename #4 ComC/ComGF > color #3 skyblue > color #4 skyblue > select add #1 2554 atoms, 2601 bonds, 326 residues, 1 model selected > select subtract #1 Nothing selected > hide #1 models > hide #2 models > hide #3 models > hide #4 models > show #2 models Alignment identifier is 1 Alignment identifier is 1/B Alignment identifier is 2/B Alignment identifier is 3/B Alignment identifier is 4/B > select #1/A:109 #2/A:109 #3/A:109 #4/A:109 32 atoms, 28 bonds, 4 residues, 4 models selected > select #1/A:109 #2/A:109 #3/A:109 #4/A:109 32 atoms, 28 bonds, 4 residues, 4 models selected . [ID: 1] region 4 chains [109] RMSD: 0.327 > style sel & #2 ball Changed 8 atom styles > show sel & #2 atoms > select #1/A:158 #2/A:158 #3/A:158 #4/A:158 32 atoms, 28 bonds, 4 residues, 4 models selected > select #1/A:158 #2/A:158 #3/A:158 #4/A:158 32 atoms, 28 bonds, 4 residues, 4 models selected . [ID: 1] region 4 chains [158] RMSD: 0.137 > style sel & #2 ball Changed 8 atom styles > show sel & #2 atoms > select #2/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B 1157 atoms, 1175 bonds, 144 residues, 1 model selected > ui tool show ""Color Actions"" > color sel peru > select #2/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/B:1-15 118 atoms, 118 bonds, 15 residues, 1 model selected > color sel gold > hide #2 models > select add #2 2906 atoms, 2965 bonds, 364 residues, 1 model selected > show #3 models > select subtract #2 Nothing selected > select #1/A:109 #2/A:109 #3/A:109 #4/A:109 32 atoms, 28 bonds, 4 residues, 4 models selected > select #1/A:109 #2/A:109 #3/A:109 #4/A:109 32 atoms, 28 bonds, 4 residues, 4 models selected . [ID: 1] region 4 chains [109] RMSD: 0.327 > style sel & #3 ball Changed 8 atom styles > show sel & #3 atoms > style sel & #3 ball Changed 8 atom styles > show sel & #3 atoms > color sel byelement > undo > color sel byhetero > select #1/A:158 #2/A:158 #3/A:158 #4/A:158 32 atoms, 28 bonds, 4 residues, 4 models selected > select #1/A:158 #2/A:158 #3/A:158 #4/A:158 32 atoms, 28 bonds, 4 residues, 4 models selected . [ID: 1] region 4 chains [158] RMSD: 0.137 > show sel & #3 atoms > style sel & #3 ball Changed 8 atom styles > color sel byhetero > select #3/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B 770 atoms, 775 bonds, 97 residues, 1 model selected > color sel rosy brown > select #3/B:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/B:1-11 89 atoms, 88 bonds, 11 residues, 1 model selected > color sel gold > select add #3 2519 atoms, 2565 bonds, 317 residues, 1 model selected > hide #3 models > select subtract #3 Nothing selected > show #4 models > select #1/A:158 #2/A:158 #3/A:158 #4/A:158 32 atoms, 28 bonds, 4 residues, 4 models selected > select #1/A:158 #2/A:158 #3/A:158 #4/A:158 32 atoms, 28 bonds, 4 residues, 4 models selected . [ID: 1] region 4 chains [158] RMSD: 0.137 > color sel byhetero > show sel & #4 atoms > style sel & #4 ball Changed 8 atom styles > select #1/A:109 #2/A:109 #3/A:109 #4/A:109 32 atoms, 28 bonds, 4 residues, 4 models selected > select #1/A:109 #2/A:109 #3/A:109 #4/A:109 32 atoms, 28 bonds, 4 residues, 4 models selected . [ID: 1] region 4 chains [109] RMSD: 0.327 > style sel & #4 ball Changed 8 atom styles > show sel & #4 atoms > select #4/B:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B 1188 atoms, 1206 bonds, 145 residues, 1 model selected > color sel crimson > select #4/B:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:1-9 73 atoms, 73 bonds, 9 residues, 1 model selected > color sel gold > select add #4 2937 atoms, 2996 bonds, 365 residues, 1 model selected > select subtract #4 Nothing selected > show #3 models > show #2 models > show #1 models > hide #1 models > show #1 models > hide #2 models > show #2 models > hide #3 models > show #3 models > hide #4 models > show #4 models > save /Users/vlad/Documents/1B.cxs ——— End of log from Thu Apr 3 14:25:32 2025 ——— opened ChimeraX session > select #1/A:1-45 #2/A:1-45 #3/A:1-45 #4/A:1-45 1412 atoms, 1452 bonds, 180 residues, 4 models selected > select #1/A #2/A #3/A #4/A 6996 atoms, 7160 bonds, 880 residues, 4 models selected . [ID: 1] region 4 chains [1-220] RMSD: 0.425 > show sel surfaces > transparency (#!1-4 & sel) 50 > transparency (#!1-4 & sel) 40 > transparency (#!1-4 & sel) 60 > hide #!2 models > hide #!3 models > hide #!4 models > select add #1 7801 atoms, 7971 bonds, 986 residues, 8 models selected > select add #2 8958 atoms, 9146 bonds, 1130 residues, 8 models selected > select add #3 9728 atoms, 9921 bonds, 1227 residues, 8 models selected > select add #4 10916 atoms, 11127 bonds, 1372 residues, 8 models selected > select subtract #4 7979 atoms, 8131 bonds, 1007 residues, 7 models selected > select subtract #3 5460 atoms, 5566 bonds, 690 residues, 5 models selected > select subtract #2 2554 atoms, 2601 bonds, 326 residues, 3 models selected > select subtract #1 1 model selected > show #!2 models > show #!3 models > show #!4 models > hide #!4 models > hide #!3 models > hide #!2 models > save /Users/vlad/Desktop/image1.png supersample 3 > hide #!1 models > show #!2 models > save /Users/vlad/Desktop/image2.png supersample 3 > hide #!2 models > show #!3 models > show #!4 models > hide #!4 models > show #!1 models > show #!2 models > hide #!3 models > show #!3 models > show #!4 models > hide #!3 models > hide #!2 models > hide #!4 models > save /Users/vlad/Desktop/image1.png supersample 3 > hide #!1 models > show #!2 models > save /Users/vlad/Desktop/image2.png supersample 3 > hide #!2 models > show #!3 models > save /Users/vlad/Desktop/image3.png supersample 3 > hide #!3 models > show #!4 models > save /Users/vlad/Desktop/image4.png supersample 3 > save /Users/vlad/Desktop/1b.cxs ——— End of log from Fri Apr 4 10:51:11 2025 ——— > view name session-start opened ChimeraX session > open ""/Users/vlad/Desktop/fig 4.pdb"" Chain information for fig 4.pdb #5 --- Chain | Description A | No description available B | No description available > hide #!4 models > show #!1 models > close #2-4 > hide #!1 models > show #!1 models Alignment identifier is 1 Alignment identifier is 1/B Alignment identifier is 5/B > select #1/A:1 #5/A:1 16 atoms, 14 bonds, 2 residues, 2 models selected > select #1/A #5/A 3497 atoms, 3579 bonds, 440 residues, 2 models selected . [ID: 1] region 2 chains [1-220] RMSD: 21.966 > save /Users/vlad/Desktop/fig.cxs ——— End of log from Mon Oct 13 15:18:41 2025 ——— > view name session-start opened ChimeraX session > show sel surfaces > transparency (#!1,5 & sel) 50 > save ""/Users/vlad/Desktop/fig 4.cxs"" ——— End of log from Mon Oct 13 15:20:03 2025 ——— > view name session-start opened ChimeraX session > color #5 #93cde9ff > close #5.1 > save /Users/vlad/Desktop/fig.cxs ——— End of log from Mon Oct 13 15:53:34 2025 ——— > view name session-start opened ChimeraX session > select add #5 3699 atoms, 3784 bonds, 464 residues, 2 models selected > select add #1 4504 atoms, 4595 bonds, 570 residues, 2 models selected > select subtract #1 1950 atoms, 1994 bonds, 244 residues, 2 models selected > select subtract #5 Nothing selected > ui tool show Matchmaker > matchmaker #5 to #1 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 ComC/ComGC, chain A (#1) with fig 4.pdb, chain A (#5), sequence alignment score = 1119.3 RMSD between 214 pruned atom pairs is 0.686 angstroms; (across all 220 pairs: 0.778) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.8.16 OpenGL renderer: Intel(R) Iris(TM) Graphics 550 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro13,2 Processor Name: Dual-Core Intel Core i7 Processor Speed: 3,3 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 529.120.1.0.0 OS Loader Version: 540.120.3~37 SMC Version (system): 2.37f25 Software: System Software Overview: System Version: macOS 12.7.6 (21H1320) Kernel Version: Darwin 21.6.0 Time since boot: 11 days 2:16 Graphics/Displays: Intel Iris Graphics 550: Chipset Model: Intel Iris Graphics 550 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x1927 Revision ID: 0x000a Metal Family: Supported, Metal GPUFamily macOS 2 Displays: BenQ PD3220U: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: YBL13415019 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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 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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect feedback normal Core Tom Goddard all ChimeraX