Opened 2 months ago

Closed 2 months ago

#18439 closed defect (duplicate)

Crash in python_instances_of_class

Reported by: herrera.alfa@… Owned by: pett
Priority: normal Milestone:
Component: Structure Editing Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.7.5-arm64-arm-64bit
ChimeraX Version: 1.8.dev202403210048 (2024-03-21 00:48:29 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000000030e8af000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030d8a3000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030c897000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030b88b000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030a87f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000309873000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000308867000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030785b000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000030684f000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000305843000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000304837000 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fcc9cf80 (most recent call first):
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 44 in python_instances_of_class
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 176 in _copy_custom_attrs
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 149 in combine
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 522 in bind
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/mod.py", line 376 in cn_peptide_bond
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/cmd.py", line 205 in cmd_join_peptide
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
  File "/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 774 in _jm_apply_cb
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/build_structure/tool.py", line 1193 in 
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, lxml._elementpath, lxml.etree, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, PIL._imagingmath (total: 59)


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{
  "uptime" : 630000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 1729093738,
  "deployVersion" : 210,
  "modelCode" : "Mac14,2",
  "coalitionID" : 43753,
  "osVersion" : {
    "train" : "macOS 14.7.5",
    "build" : "23H527",
    "releaseType" : "User"
  },
  "captureTime" : "2025-08-14 12:33:33.7225 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "ED5743AD-FBE5-4269-BB2A-A4422A2755A2",
  "pid" : 19726,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2025-08-14 12:10:29.7402 -0500",
  "procStartAbsTime" : 15127511632907,
  "procExitAbsTime" : 15160726214226,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"84939D93-11DF-572A-B9E1-4AFEBE55A994","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "D838229F-FA46-F28D-A6DE-DAAA28E4700D",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 94073,
  "sleepWakeUUID" : "50C948D9-D3CF-4221-BBCA-C38458D40500",
  "sip" : "enabled",
  "vmRegionInfo" : "0x10c0139 is not in any region.  Bytes before following region: 4324736711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102d24000-102d28000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "exception" : {"codes":"0x0000000000000001, 0x00000000010c0139","rawCodes":[1,17563961],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000010c0139"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":19726},
  "vmregioninfo" : "0x10c0139 is not in any region.  Bytes before following region: 4324736711\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      102d24000-102d28000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
  "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" : [{"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":4697914008},{"value":80},{"value":95},{"value":0},{"value":0},{"value":16361926975594471944},{"value":16361926974332562824},{"value":14757395258967641293},{"value":4294967286},{"value":4697913938},{"value":0},{"value":53},{"value":4294967280},{"value":328},{"value":8711154688},{"value":0},{"value":11},{"value":8536051584,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8536051808,"symbolLocation":224,"symbol":"_main_thread"},{"value":1},{"value":4365387312,"symbolLocation":0,"symbol":"faulthandler_handlers"},{"value":0},{"value":1},{"value":1},{"value":6124569680}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6792916000},"cpsr":{"value":1073745920},"fp":{"value":4697914080},"sp":{"value":4697914048},"esr":{"value":1442840704,"description":" Address size 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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Compositor returned null texture  

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/workingon.closed0716.cxs" format session

opened ChimeraX session  

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"

opened ChimeraX session  

> hide #!9 models

> hide #53 models

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> log metadata #105

The model has no metadata

> log chains #105

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105  
---  
Chain | Description  
A | No description available  
  

> sequence chain #105/A

Alignment identifier is 105/A  

> select #105/A:1999-2000

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select #105/A:1800-2000

3081 atoms, 3109 bonds, 201 residues, 1 model selected  
No visible models!  

> show #105 models

> select #105/A:1999-2000

28 atoms, 28 bonds, 2 residues, 1 model selected  

> select #105/A:1800-2000

3081 atoms, 3109 bonds, 201 residues, 1 model selected  

> show sel cartoons

> delete atoms sel

> delete bonds sel

> select #105/A:2093

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #105/A:2093-2094

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #105/A:2001

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #105/A:2001

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select add #105

21063 atoms, 21226 bonds, 1400 residues, 1 model selected  

> select subtract #105

Nothing selected  

> hide #105 models

> show #104 models

> show #105 models

> show #110 models

> show #111 models

> select #104/A:1

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #104/A:1-123

1934 atoms, 1957 bonds, 123 residues, 1 model selected  

> select #105/A:2001

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #105/A:2001-2146

2178 atoms, 2196 bonds, 146 residues, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #104/A:1936-1999

988 atoms, 996 bonds, 64 residues, 1 model selected  

> hide #110 models

> hide #111 models

> hide #105 models

> select add #104

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #104

Nothing selected  

> hide #104 models

> show #108 models

> show #107 models

> hide #107 models

> hide #108 models

> show #104 models

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> color sel lime

> select add #104

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #104

Nothing selected  

> show #105 models

> select #105/A:2089

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select #105/A:2080-2089

156 atoms, 155 bonds, 10 residues, 1 model selected  

> select #105/A:2075-2079

59 atoms, 58 bonds, 5 residues, 1 model selected  

> select #105/A:2020-2079

927 atoms, 933 bonds, 60 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #105,0.070652,0.61953,-0.78179,69.828,-0.84869,0.44916,0.27924,75.159,0.52415,0.64377,0.55752,92.604

> view matrix models
> #105,0.070652,0.61953,-0.78179,76.425,-0.84869,0.44916,0.27924,84.784,0.52415,0.64377,0.55752,100.34

> select #105/A:2265-2319

827 atoms, 833 bonds, 55 residues, 1 model selected  

> select #105/A:2265-2367

1546 atoms, 1554 bonds, 103 residues, 1 model selected  

> select #105/A:2265

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

> select #105/A:2265-2319

827 atoms, 833 bonds, 55 residues, 1 model selected  

> select #105/A:2001

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select #105/A:2001

10 atoms, 9 bonds, 1 residue, 1 model selected  

> color sel red

> ui mousemode right "rotate selected models"

> view matrix models
> #105,-0.26571,0.91879,-0.29193,74.464,0.36029,-0.18624,-0.91406,93.006,-0.8942,-0.34806,-0.28154,86.054

> view matrix models
> #105,-0.13796,0.94724,-0.28933,75.613,0.57439,-0.16147,-0.8025,95.483,-0.80687,-0.2769,-0.52181,85.593

> view matrix models
> #105,-0.17164,0.94046,-0.29339,75.293,0.52077,-0.16619,-0.83737,94.827,-0.83627,-0.29651,-0.46124,85.644

> view matrix models
> #105,-0.18698,0.9372,-0.29444,75.151,0.49567,-0.16877,-0.85196,94.529,-0.84815,-0.30525,-0.43298,85.684

> view matrix models
> #105,-0.24492,0.92393,-0.29389,74.639,0.39713,-0.18093,-0.89975,93.407,-0.88448,-0.33708,-0.3226,85.929

> view matrix models
> #105,-0.18093,0.9385,-0.29409,75.207,0.50562,-0.16772,-0.8463,94.647,-0.84357,-0.30182,-0.44418,85.667

> view matrix models
> #105,-0.22163,0.92945,-0.29498,74.84,0.43746,-0.17558,-0.88193,93.857,-0.8715,-0.3245,-0.36768,85.812

> ui mousemode right "translate selected models"

> view matrix models
> #105,-0.22163,0.92945,-0.29498,62.302,0.43746,-0.17558,-0.88193,86.244,-0.8715,-0.3245,-0.36768,47.764

> select add #105

21063 atoms, 21226 bonds, 1400 residues, 1 model selected  

> select subtract #105

Nothing selected  

> ui mousemode right select

Drag select of 2 residues  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small

> select add #104

51426 atoms, 51864 bonds, 3399 residues, 1 model selected  

> select subtract #104

Nothing selected  

> select add #104

51426 atoms, 51864 bonds, 3399 residues, 1 model selected  

> select subtract #104

Nothing selected  

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> select clear

> delete atoms #104

> delete bonds #104

> undo

> close session

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"

opened ChimeraX session  

> hide #!9 models

> hide #53 models

> show #105 models

> hide #105 models

> show #105 models

> log metadata #105

The model has no metadata

> log chains #105

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105  
---  
Chain | Description  
A | No description available  
  

> sequence chain #105/A

Alignment identifier is 105/A  

> select #105/A:2000

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select #105/A:1800-2000

3081 atoms, 3109 bonds, 201 residues, 1 model selected  

> show #104 models

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> select #105/A:1899

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #105/A:1800-1899

1560 atoms, 1573 bonds, 100 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> rename #105 GMGC10.011_528_202.ranked_0.1900.3500.pdb

> select clear

> delete atoms #104-105

> delete bonds #104-105

> close session

> open "/Users/aho2840/Desktop/Satchell
> Lab/MCFHomologs/MCF:Homolog.paper/Homologs.08.11.25.cxs"

opened ChimeraX session  

> hide #!9 models

> hide #53 models

> show #105 models

> log metadata #105

The model has no metadata

> log chains #105

Chain information for GMGC10.011_528_202.ranked_0.1800.3500.pdb #105  
---  
Chain | Description  
A | No description available  
  

> sequence chain #105/A

Alignment identifier is 105/A  

> log metadata #104

The model has no metadata

> log chains #104

Chain information for GMGC10.011_528_202.ranked_0.1.2000.ranked_0.pdb #104  
---  
Chain | Description  
A | No description available  
  

> sequence chain #104/A

Alignment identifier is 104/A  

> select #105/A:1899

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select #105/A:1800-1899

1560 atoms, 1573 bonds, 100 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select #105/A:2037

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select #105/A:2037-2039

55 atoms, 55 bonds, 3 residues, 1 model selected  

> select add #105

22584 atoms, 22762 bonds, 1501 residues, 1 model selected  

> select subtract #105

Nothing selected  

> hide #105 models

> show #104 models

> select clear

> ui mousemode right "translate selected models"

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> select #104/A:1999

18 atoms, 17 bonds, 1 residue, 1 model selected  

> color sel lime

> ui mousemode right "rotate selected models"

> view matrix models
> #104,0.29294,-0.94332,-0.15599,32.47,0.67976,0.090735,0.7278,21.614,-0.6724,-0.31924,0.66781,-17.296

> view matrix models
> #104,0.70895,-0.70178,-0.06998,26.296,-0.17643,-0.27255,0.94583,23.607,-0.68283,-0.6582,-0.31704,9.5095

> select add #104

30364 atoms, 30638 bonds, 1999 residues, 1 model selected  

> select subtract #104

Nothing selected  

> show #105 models

> ui mousemode right "translate selected models"

> select #105/A:1983-2037

893 atoms, 903 bonds, 55 residues, 1 model selected  

> select #105/A:1972-1983

175 atoms, 176 bonds, 12 residues, 1 model selected  

> view matrix models
> #105,0.070652,0.61953,-0.78179,-50.196,-0.84869,0.44916,0.27924,33.335,0.52415,0.64377,0.55752,46.74

> view matrix models
> #105,0.070652,0.61953,-0.78179,-78.989,-0.84869,0.44916,0.27924,9.2126,0.52415,0.64377,0.55752,56.82

> select #105/A:1900

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #105/A:1900

16 atoms, 15 bonds, 1 residue, 1 model selected  

> color sel red

> view matrix models
> #105,0.070652,0.61953,-0.78179,-83.665,-0.84869,0.44916,0.27924,30.632,0.52415,0.64377,0.55752,25.148

> select #105/A:1900

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select #105/A:1900-2445

8224 atoms, 8285 bonds, 546 residues, 1 model selected  

> show sel cartoons

> select add #105

22584 atoms, 22762 bonds, 1501 residues, 1 model selected  

> select subtract #105

Nothing selected  

> select #105/A:2094-2095

36 atoms, 35 bonds, 2 residues, 1 model selected  

> select #105/A:2029-2095

1009 atoms, 1013 bonds, 67 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #105,0.92879,-0.037345,0.36873,-68.4,-0.065942,-0.99569,0.065259,41.702,0.3647,-0.084927,-0.92724,19.441

> ui mousemode right "translate selected models"

> view matrix models
> #105,0.92879,-0.037345,0.36873,-74.092,-0.065942,-0.99569,0.065259,27.971,0.3647,-0.084927,-0.92724,58.477

> view matrix models
> #105,0.92879,-0.037345,0.36873,-72.83,-0.065942,-0.99569,0.065259,27.978,0.3647,-0.084927,-0.92724,58.484

> ui mousemode right select

Drag select of 2 residues  

> ui tool show "Build Structure"

> build join peptide sel length 1.33 omega 180 phi -120 move small


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

Log:
UCSF ChimeraX version: 1.8.dev202403210048 (2024-03-21)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z160000B1LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.101.1
      OS Loader Version: 10151.140.19.700.2

Software:

    System Software Overview:

      System Version: macOS 14.7.5 (23H527)
      Kernel Version: Darwin 23.6.0
      Time since boot: 28 days, 15 hours, 20 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.14.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.1.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.16
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.3
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.5
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.56
    ChimeraX-AtomicLibrary: 14.0.2
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8.dev202403210048
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    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-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.3
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.3
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    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: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.37.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.9
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.1
    fonttools: 4.50.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2024.2.26
    idna: 3.6
    ihm: 0.43
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    Jinja2: 3.1.3
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.1.0
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.8
    ndindex: 1.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.2.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.9.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.3
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.2.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.3.0
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3302
    pyparsing: 3.1.2
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.2
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.2
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 25.1.2
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.12.0
    setuptools: 69.2.0
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.0
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.1
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.1
    typing-extensions: 4.10.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (2)

comment:1 by Tom Goddard, 2 months ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in python_instances_of_class

Duplicate of #18437

comment:2 by Tom Goddard, 2 months ago

Resolution: → duplicate
Status: assigned → closed
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