Opened 9 months ago

Closed 9 months ago

#16810 closed defect (can't reproduce)

Crash getting StructureSeq.structure

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
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-12.7.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x0000000102b04580 (most recent call first):
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 91 in get_prop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1255 in _changes_cb
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1069 in proxy_handler
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 54 in check_for_changes
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py", line 77 in 
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3318 in command_trigger
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 144 in __exit__
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3203 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 225 in delete
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py", line 308 in _key_closed
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py", line 105 in delete
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py", line 1013 in close
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/close.py", line 43 in close
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 517 in close
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/model_panel/tool.py", line 92 in 
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
  File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 56)


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{
  "uptime" : 430000,
  "procLaunch" : "2025-02-07 11:42:36.8532 -0500",
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,3",
  "procStartAbsTime" : 10312202245463,
  "coalitionID" : 35419,
  "osVersion" : {
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  "captureTime" : "2025-02-07 11:57:36.7066 -0500",
  "incident" : "1E19A661-8483-4835-900E-917D79006555",
  "bug_type" : "309",
  "pid" : 74414,
  "procExitAbsTime" : 10333795704744,
  "translated" : false,
  "cpuType" : "ARM-64",
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"D055974A-FA62-5EFA-B77F-2A36D66C8CF9","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "64133C3A-46C4-C443-3C1A-7D431FADF00B",
  "wakeTime" : 1808,
  "sleepWakeUUID" : "1CB59322-17D2-4A98-BA4E-53FFD1797B8A",
  "sip" : "enabled",
  "vmRegionInfo" : "0xfffffffffffffff8 is not in any region.  Bytes after previous region: 18446638519519543289  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO (reserved)   600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)\n--->  \n      UNUSED SPACE AT END",
  "isCorpse" : 1,
  "exception" : {"codes":"0x0000000000000001, 0x5ffffffffffffff8","rawCodes":[1,6917529027641081848],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x5ffffffffffffff8 -> 0xfffffffffffffff8 (possible pointer authentication failure)"},
  "ktriageinfo" : "VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n",
  "vmregioninfo" : "0xfffffffffffffff8 is not in any region.  Bytes after previous region: 18446638519519543289  \n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      MALLOC_NANO (reserved)   600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)\n--->  \n      UNUSED SPACE AT END",
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    "base" : 4347985920,
    "size" : 81920,
    "uuid" : "6c214dd2-6044-3285-949b-8d8ba72ca17b",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_ctypes.cpython-311-darwin.so",
    "name" : "_ctypes.cpython-311-darwin.so"
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    "base" : 4548722688,
    "size" : 1769472,
    "uuid" : "96b797fa-3120-323b-9d82-a251f6e48226",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/QtCore.abi3.so",
    "name" : "QtCore.abi3.so"
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  {
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    "arch" : "arm64",
    "base" : 4809801728,
    "size" : 4603904,
    "uuid" : "5e316915-192d-32ae-b085-7c0986279324",
    "path" : "\/Applications\/ChimeraX-1.9.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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    "arch" : "arm64",
    "base" : 5079351296,
    "size" : 4620288,
    "uuid" : "6b195f36-d220-34c8-afd3-7caa96572118",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWidgets.framework\/Versions\/A\/QtWidgets",
    "name" : "QtWidgets"
  },
  {
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    "arch" : "arm64",
    "base" : 4822401024,
    "size" : 3080192,
    "uuid" : "ac9bb37f-d5ad-31aa-8307-d081879d1aef",
    "path" : "\/Applications\/ChimeraX-1.9.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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    "arch" : "arm64",
    "base" : 5066719232,
    "size" : 6635520,
    "uuid" : "3efe39e7-026f-3417-94b4-be4f2ec95e51",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtGui.framework\/Versions\/A\/QtGui",
    "name" : "QtGui"
  },
  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 5267292160,
    "size" : 655360,
    "uuid" : "fab03cd7-ccd1-33ab-bc97-91ce7e4911a2",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/plugins\/platforms\/libqcocoa.dylib",
    "name" : "libqcocoa.dylib"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6892863488,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.CoreFoundation",
    "size" : 5533696,
    "uuid" : "07e05b49-8c3c-354e-89a7-cc7994572dfe",
    "path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
    "name" : "CoreFoundation",
    "CFBundleVersion" : "1866"
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  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 7040278528,
    "CFBundleShortVersionString" : "2.1.1",
    "CFBundleIdentifier" : "com.apple.HIToolbox",
    "size" : 3358720,
    "uuid" : "07987381-b579-3f72-8ba8-97fa5b5a3352",
    "path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
    "name" : "HIToolbox"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 6938648576,
    "CFBundleShortVersionString" : "6.9",
    "CFBundleIdentifier" : "com.apple.AppKit",
    "size" : 15437824,
    "uuid" : "f22b39bd-c01b-3a5a-a7f6-190cb4e425cc",
    "path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
    "name" : "AppKit",
    "CFBundleVersion" : "2113.60.148"
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    "source" : "P",
    "arch" : "arm64",
    "base" : 4335665152,
    "CFBundleShortVersionString" : "1.9.0",
    "CFBundleIdentifier" : "edu.ucsf.cgl.ChimeraX",
    "size" : 16384,
    "uuid" : "17982d98-65bc-3327-8526-577ec996453c",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
    "name" : "ChimeraX",
    "CFBundleVersion" : "1.9.0.0"
  },
  {
    "source" : "P",
    "arch" : "arm64e",
    "base" : 4339580928,
    "size" : 393216,
    "uuid" : "83d4a362-5b15-3bd4-98f4-54861eb4da38",
    "path" : "\/usr\/lib\/dyld",
    "name" : "dyld"
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  {
    "source" : "P",
    "arch" : "arm64",
    "base" : 11125424128,
    "size" : 173883392,
    "uuid" : "309d9313-74e8-3f16-8acc-0f13b36d8e00",
    "path" : "\/Applications\/ChimeraX-1.9.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
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    "base" : 6908612608,
    "CFBundleShortVersionString" : "6.9",
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    "size" : 4136960,
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    "path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
    "name" : "Foundation",
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    "path" : "\/Applications\/ChimeraX-1.9.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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  {
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    "source" : "A",
    "base" : 0,
    "uuid" : "00000000-0000-0000-0000-000000000000"
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],
  "sharedCache" : {
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  "size" : 3144908800,
  "uuid" : "5408e7f4-3e59-3617-afe0-a77be4627ee5"
},
  "vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n                                VIRTUAL   REGION \nREGION TYPE                        SIZE    COUNT (non-coalesced) \n===========                     =======  ======= \nAccelerate framework               512K        4 \nActivity Tracing                   256K        1 \nCG backing stores                 7360K        8 \nCG image                           336K       14 \nColorSync                          640K       28 \nCoreAnimation                      464K       23 \nCoreGraphics                        48K        3 \nCoreUI image data                 4304K       30 \nFoundation                          48K        2 \nKernel Alloc Once                   32K        1 \nMALLOC                             1.3G      223 \nMALLOC guard page                  192K       11 \nMALLOC_MEDIUM (reserved)         952.0M       10         reserved VM address space (unallocated)\nMALLOC_NANO (reserved)           384.0M        1         reserved VM address space (unallocated)\nMach message                        64K        3 \nOpenGL GLSL                        384K        4 \nSTACK GUARD                        640K       40 \nStack                            193.9M       41 \nStack Guard                       56.0M        1 \nVM_ALLOCATE                      227.5M      190 \nVM_ALLOCATE (reserved)           192.0M        3         reserved VM address space (unallocated)\n__AUTH                            2686K      344 \n__AUTH_CONST                      21.4M      554 \n__CTF                               756        1 \n__DATA                            25.3M      731 \n__DATA_CONST                      30.2M      737 \n__DATA_DIRTY                      1968K      242 \n__FONT_DATA                          4K        1 \n__GLSLBUILTINS                    5176K        1 \n__LINKEDIT                       613.1M      182 \n__OBJC_CONST                      4022K      320 \n__OBJC_RO                         83.0M        1 \n__OBJC_RW                         3168K        1 \n__TEXT                           796.3M      755 \n__UNICODE                          592K        1 \ndyld private memory               1072K        3 \nmapped file                      197.8M       49 \nshared memory                     3152K       22 \n===========                     =======  ======= \nTOTAL                              5.0G     4586 \nTOTAL, minus reserved VM space     3.6G     4586 \n",
  "legacyInfo" : {
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},
  "trialInfo" : {
  "rollouts" : [
    {
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      "factorPackIds" : {

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}
}
===== Log before crash start =====
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/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
> rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/2025_02_05_23_55_drome/fold_2025_02_05_23_55_drome_model_0.cif

Chain information for fold_2025_02_05_23_55_drome_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open /Users/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
> rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/2025_02_05_23_55_human/fold_2025_02_05_23_55_human_model_0.cif

Chain information for fold_2025_02_05_23_55_human_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open /Users/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
> rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/2025_02_05_23_56_mouse/fold_2025_02_05_23_56_mouse_model_0.cif

Chain information for fold_2025_02_05_23_56_mouse_model_0.cif #3  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open /Users/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
> rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/2025_02_05_23_57_bovin/fold_2025_02_05_23_57_bovin_model_0.cif

Chain information for fold_2025_02_05_23_57_bovin_model_0.cif #4  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> open /Users/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
> rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/2025_02_05_23_57_yeast/fold_2025_02_05_23_57_yeast_model_0.cif

Chain information for fold_2025_02_05_23_57_yeast_model_0.cif #5  
---  
Chain | Description  
A | .  
B | .  
  
Computing secondary structure  

> lighting soft

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> mmaker #1-4 to #5/A

Computing secondary structure  
Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2025_02_05_23_57_yeast_model_0.cif, chain A (#5) with
fold_2025_02_05_23_55_drome_model_0.cif, chain A (#1), sequence alignment
score = 910.7  
RMSD between 278 pruned atom pairs is 1.091 angstroms; (across all 436 pairs:
9.912)  
  
Matchmaker fold_2025_02_05_23_57_yeast_model_0.cif, chain A (#5) with
fold_2025_02_05_23_55_human_model_0.cif, chain A (#2), sequence alignment
score = 1021.1  
RMSD between 281 pruned atom pairs is 0.931 angstroms; (across all 477 pairs:
21.581)  
  
Matchmaker fold_2025_02_05_23_57_yeast_model_0.cif, chain A (#5) with
fold_2025_02_05_23_56_mouse_model_0.cif, chain A (#3), sequence alignment
score = 1005.2  
RMSD between 281 pruned atom pairs is 0.930 angstroms; (across all 479 pairs:
20.101)  
  
Matchmaker fold_2025_02_05_23_57_yeast_model_0.cif, chain A (#5) with
fold_2025_02_05_23_57_bovin_model_0.cif, chain A (#4), sequence alignment
score = 1041.2  
RMSD between 279 pruned atom pairs is 0.916 angstroms; (across all 487 pairs:
22.921)  
  

> color bychain

> hide #1-4 target m

> lighting soft

> color @@bfactor /B

> color @@bfactor

> color @@bfactor>80

> select @@bfactor>80

15124 atoms, 15257 bonds, 2428 residues, 5 models selected  

> color byattribute

Missing or invalid "attrName" argument: Expected a text string  

> color byattribute bfactor

37120 atoms, 4731 residues, atom bfactor range 11.1 to 97.7  

> color byattribute bfactor palette alphafold

37120 atoms, 4731 residues, atom bfactor range 11.1 to 97.7  

> color bychain

> color byattribute bfactor /B palette alphafold

17268 atoms, 2194 residues, atom bfactor range 11.1 to 92  

> select clear

> color bychain

> color bypolymer

> show #4 models

> hide #5 models

> show #5 models

> show #3 models

> hide #4 models

> hide #5 models

> hide #3 models

> show #3 models

> show #5 models

> hide #3 models

> color white

> color byattribute bfactor /B palette alphafold

17268 atoms, 2194 residues, atom bfactor range 11.1 to 92  

> color byattribute bfactor /B palette alphafold key true

> key alphafold :0 :50 :70 :90 :100 showTool true

> ui mousemode right "color key"

17268 atoms, 2194 residues, atom bfactor range 11.1 to 92  

> show #4 models

> hide #5 models

> show #3 models

> hide #4 models

> show #2 models

> hide #3 models

> show #1 models

> hide #2 models

> open /Users/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
> rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/nop12_aligment.clustal

Summary of feedback from opening
/Users/rafalpiwowarczyk/Library/CloudStorage/OneDrive-
rockefeller.edu/KlingeLab/DATA/20250205-Pwp1-Nop12-aligmnets/nop12_aligment.clustal  
---  
notes | Alignment identifier is nop12_aligment.clustal  
Associated fold_2025_02_05_23_55_drome_model_0.cif chain B to UniRef90_Q9VJG2
with 0 mismatches  
Associated fold_2025_02_05_23_55_human_model_0.cif chain B to
sp|P42696|RBM34_HUMAN with 0 mismatches  
Associated fold_2025_02_05_23_56_mouse_model_0.cif chain B to
sp|Q8C5L7|RBM34_MOUSE with 0 mismatches  
Associated fold_2025_02_05_23_57_bovin_model_0.cif chain B to UniRef90_F6QT33
with 0 mismatches  
Associated fold_2025_02_05_23_57_yeast_model_0.cif chain B to
sp|Q08208|NOP12_YEAST with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment nop12_aligment.clustal  
  
Opened 6 sequences from nop12_aligment.clustal  

> hide #1 models

> show #5 models

> set bgColor white

> set bgColor black

> select #5/B:25

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #5/B:25

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #5/B:1-25

195 atoms, 196 bonds, 25 residues, 1 model selected  

> select #3/B:70

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #3/B:33-70

260 atoms, 267 bonds, 38 residues, 1 model selected  

> select #5/B:37

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/B:1-37

279 atoms, 281 bonds, 37 residues, 1 model selected  

> select #5/B:1

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #5/B:1-37 #3/B:33-70 #2/B:35-72 #4/B:35-72

1110 atoms, 1130 bonds, 151 residues, 4 models selected  
Nop12_aligment.clustal [ID: nop12_aligment.clustal] region
sp|Q08208|NOP12_YEAST..UniRef90_F6QT33 [35-72] RMSD: 6.267  
  

> select #4/B:72

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/B:1-19 #5/B:1-37 #3/B:33-70 #2/B:35-72 #4/B:35-72

1261 atoms, 1282 bonds, 170 residues, 5 models selected  
Nop12_aligment.clustal [ID: nop12_aligment.clustal] region
UniRef90_Q9VJG2..UniRef90_F6QT33 [35-72] RMSD: 25.027  
  

> hide #5 models

> show #1 models

> close

> ui mousemode right translate


===== Log before crash end =====

Log:
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  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 10151.41.12
      OS Loader Version: 7459.141.1.701.1

Software:

    System Software Overview:

      System Version: macOS 12.7.1 (21G920)
      Kernel Version: Darwin 21.6.0
      Time since boot: 8 days 15:40

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        U28E590:
          Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus)
          UI Looks like: 2560 x 1440 @ 30.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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
    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-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 9 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash getting StructureSeq.structure

comment:2 by Eric Pettersen, 9 months ago

Resolution: → can't reproduce
Status: accepted → closed

Possibly fixed by recent changes in atomic (copied Structure seq with null structure produces Sequence).

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