Opened 5 days ago

Last modified 4 days ago

#19117 feedback defect

Crash in event loop

Reported by: vladimir.pelicic@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 58)


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{
  "uptime" : 170000,
  "procLaunch" : "2025-10-13 15:54:01.0714 +0200",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro13,2",
  "procStartAbsTime" : 170217124550353,
  "coalitionID" : 25785,
  "osVersion" : {
    "train" : "macOS 12.7.6",
    "build" : "21H1320",
    "releaseType" : "User"
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  "captureTime" : "2025-10-13 15:54:45.8991 +0200",
  "incident" : "E7B64521-5698-4E8C-AEEE-77FB32371360",
  "bug_type" : "309",
  "pid" : 32182,
  "procExitAbsTime" : 170261813542852,
  "cpuType" : "X86-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.10.1","CFBundleVersion":"1.10.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"2509B253-D9F7-5323-A064-BCE5731D5C1D","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "AD8C391B-6F33-95E9-406C-D207DEB490D3",
  "wakeTime" : 7803,
  "bridgeVersion" : {"build":"14Y910","train":"3.0"},
  "sleepWakeUUID" : "0D652A42-23E0-46AC-BA32-68AC42EAE780",
  "sip" : "enabled",
  "vmRegionInfo" : "0xc5e315bffb0 is not in any region.  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.  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  ",
  "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
  "faultingThread" : 0,
  "threads" : 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    "size" : 3096576,
    "uuid" : "913d3d2e-4e4c-3907-98fe-8f4abd551297",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15269888,
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    "name" : "AppKit",
    "CFBundleVersion" : "2113.65.150"
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    "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
    "name" : "QtCore"
  },
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    "size" : 2863104,
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    "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtWidgets.abi3.so",
    "name" : "QtWidgets.abi3.so"
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    "size" : 16384,
    "uuid" : "f855cdda-9ed8-308a-81a6-2e57ba7af811",
    "path" : "\/Applications\/ChimeraX-1.10.1.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.10.1.0"
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    "path" : "\/usr\/lib\/dyld",
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    "size" : 200445952,
    "uuid" : "a86c7ae2-0ab4-329f-96a5-799c662db2d5",
    "path" : "\/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"
  },
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    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.Foundation",
    "size" : 3919872,
    "uuid" : "61133096-d5f9-34bd-94b1-1e526ea018b1",
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    "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"
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],
  "sharedCache" : {
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  "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 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      144.1M      180 \n__CTF                               756        1 \n__DATA                            42.7M      727 \n__DATA_CONST                      43.1M      457 \n__DATA_DIRTY                      1805K      238 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       676.5M      155 \n__OBJC_RO                         82.9M        1 \n__OBJC_RW                         3200K        2 \n__TEXT                           883.0M      724 \n__UNICODE                          592K        1 \ndyld private memory               1104K        3 \nmapped file                      200.9M       48 \nshared memory                     2976K       26 \n===========                     =======  ======= \nTOTAL                              3.1G     3020 \nTOTAL, minus reserved VM space     2.7G     3020 \n",
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}
===== Log before crash start =====
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
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    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
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    widgetsnbextension: 4.0.14

Change History (4)

comment:1 by pett, 5 days ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by pett, 5 days ago

Status: accepted → feedback

Hi Vladimir,

Thanks for reporting this problem. Do you remember what was happening when the crash occurred? Did MatchMaker finish completely and you were starting to do something else, or was MatchMaker still running when the crash happened?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by vladimir.pelicic@…, 4 days ago 

Hi Eric,

The crash happens repeatedly when you hit the OK button.

Vladimir.

comment:4 by pett, 4 days ago

So if I'm reading the log from the ticket right, when you matchmaker fig 4.pdb to ComC/ComGC (a.k.a. fold_comc_comgc_model_0.cif) ChimeraX always crashes before matchmaker finishes and you can do anything else in ChimeraX. Is that right? If so, is there any chance I can access the fig 4.pdb and fold_comc_comgc_model_0.cif files?

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