Opened 15 months ago

Closed 15 months ago

#15662 closed defect (duplicate)

Crash in garbage collection

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-13.5-arm64-arm-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00000002bd383000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002bc377000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002bb36b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002ba35f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b9353000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b8347000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b733b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b632f000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b5323000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b4317000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b330b000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002b08cf000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002af8c3000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002ae8b7000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000002ad8ab000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001fdbe2080 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/orderedset.py", line 47 in __init__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 178 in __init__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 341 in add_trigger
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1063 in __init__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1129 in __copy__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/copy.py", line 84 in copy
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 96 in clone_seq
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 60 in matches_to_gapped_seqs
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alignment_algs/NeedlemanWunsch/__init__.py", line 55 in nw
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py", line 78 in align
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py", line 406 in match
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/match_maker/match.py", line 742 in cmd_match
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3468 in __call__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2929 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.7.1.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-1.7.1.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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree (total: 66)


{"app_name":"ChimeraX","timestamp":"2024-07-24 13:26:33.00 -0700","app_version":"1.7.1","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.7.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5 (22G74)","roots_installed":0,"name":"ChimeraX","incident_id":"05DC573B-CEBD-4587-9A34-2C2E894C0174"}
{
  "uptime" : 190000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "Mac14,6",
  "coalitionID" : 4194,
  "osVersion" : {
    "train" : "macOS 13.5",
    "build" : "22G74",
    "releaseType" : "User"
  },
  "captureTime" : "2024-07-24 13:26:31.4335 -0700",
  "incident" : "05DC573B-CEBD-4587-9A34-2C2E894C0174",
  "pid" : 50437,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-07-24 09:07:45.0700 -0700",
  "procStartAbsTime" : 4277518533293,
  "procExitAbsTime" : 4638133256056,
  "procName" : "ChimeraX",
  "procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "bundleInfo" : {"CFBundleShortVersionString":"1.7.1","CFBundleVersion":"1.7.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
  "storeInfo" : {"deviceIdentifierForVendor":"D4A651AD-227C-55E0-B00C-C264D8671D4C","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "8BF27F0C-B423-AB5C-E06A-84A1CD5778C3",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 0,
  "wakeTime" : 10260,
  "sleepWakeUUID" : "128D6A82-13C9-42A2-984E-DA64DBBD2BDB",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 105556740144983\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   6000d8000000-6000e0000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
  "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":50437},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 105556740144983\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   6000d8000000-6000e0000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "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},
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===== Log before crash start =====
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  

> lighting soft

> graphics silhouettes true

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/benjaminadler/Downloads/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif

Chain information for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif #1  
---  
Chain | Description  
A B C D E F | .  
  

> hide atoms

> show cartoons

> color bfactor

16890 atoms, 2208 residues, atom bfactor range 14.3 to 91.2  

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_A SES surface
#1.1: minimum, -13.37, mean 0.11, maximum 15.43  
Coulombic values for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_B SES surface
#1.2: minimum, -15.92, mean 0.14, maximum 15.37  
Coulombic values for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_C SES surface
#1.3: minimum, -19.48, mean 0.12, maximum 15.34  
Coulombic values for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_D SES surface
#1.4: minimum, -15.77, mean 0.12, maximum 15.40  
Coulombic values for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_E SES surface
#1.5: minimum, -17.76, mean 0.17, maximum 15.02  
Coulombic values for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif_F SES surface
#1.6: minimum, -12.37, mean 0.10, maximum 15.17  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow

> open
> /Users/benjaminadler/Downloads/fold_2024_05_30_11_34_goslar_gp218_gp061_innerbody_3mer/fold_2024_05_30_11_34_goslar_gp218_gp061_innerbody_3mer_model_0.cif

Chain information for
fold_2024_05_30_11_34_goslar_gp218_gp061_innerbody_3mer_model_0.cif #2  
---  
Chain | Description  
A B C | .  
D E F | .  
  

> hide #!1 models

> open
> /Users/benjaminadler/Downloads/fold_2024_05_30_11_17_goslar_gp218_gp219_innerbody_redo_3mer/fold_2024_05_30_11_17_goslar_gp218_gp219_innerbody_redo_3mer_model_0.cif

Chain information for
fold_2024_05_30_11_17_goslar_gp218_gp219_innerbody_redo_3mer_model_0.cif #3  
---  
Chain | Description  
A B C | .  
D E F | .  
  

> hide #2 models

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp219_6mer/fold_goslar_gp219_6mer_model_0.cif

Chain information for fold_goslar_gp219_6mer_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
  

> hide #3 models

> hide #4 atoms

> show #4 cartoons

> lighting soft

> close #3

> close

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_6_6mer/fold_goslar_gp219_gp061_6_6mer_model_0.cif

Chain information for fold_goslar_gp219_gp061_6_6mer_model_0.cif #1  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_6_6mer/fold_goslar_gp219_gp061_6_6mer_model_1.cif

Chain information for fold_goslar_gp219_gp061_6_6mer_model_1.cif #2  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_6_6mer/fold_goslar_gp219_gp061_6_6mer_model_2.cif

Chain information for fold_goslar_gp219_gp061_6_6mer_model_2.cif #3  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> hide #3 models

> hide #2 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> show #1 models

> hide #3 models

> color bfactor #1

31848 atoms, 4098 residues, atom bfactor range 19.7 to 91.1  

> rainbow #1

> show #1 surfaces

> color #!1 bychain

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp060_6mer/fold_goslar_gp060_6mer_model_0.cif

Chain information for fold_goslar_gp060_6mer_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
  

> hide #!1 models

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061_gp060_6_6mer/fold_goslar_gp061_gp060_6_6mer_model_0.cif

Chain information for fold_goslar_gp061_gp060_6_6mer_model_0.cif #5  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> hide #4 models

> show #!1 models

> mmaker #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 fold_goslar_gp219_gp061_6_6mer_model_0.cif, chain G (#1) with
fold_goslar_gp061_gp060_6_6mer_model_0.cif, chain A (#5), sequence alignment
score = 1826.2  
RMSD between 250 pruned atom pairs is 0.780 angstroms; (across all 368 pairs:
7.641)  
  

> show #5#!1 surfaces

> hide #!1 models

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_gp060_2_2_2mer/fold_goslar_gp219_gp061_gp060_2_2_2mer_model_0.cif

Chain information for fold_goslar_gp219_gp061_gp060_2_2_2mer_model_0.cif #6  
---  
Chain | Description  
A B | .  
C D | .  
E F | .  
  

> hide #!5 models

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061_gp060_6_6mer/fold_goslar_gp061_gp060_6_6mer_model_0.cif

Chain information for fold_goslar_gp061_gp060_6_6mer_model_0.cif #7  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> hide #6 models

> show #!1 models

> hide #7 models

> show #!5 models

> select #5/G:1

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

> select #5/H:1

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

> select #5/F:1

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

> color sel magenta

> hide #!1 models

> select #5

31236 atoms, 31674 bonds, 4008 residues, 1 model selected  

> rainbow sel

> color bfactor sel

31236 atoms, 4008 residues, 12 surfaces, atom bfactor range 15.6 to 89.6  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp219_gp061_gp060_2_6_2mer/fold_goslar_gp219_gp061_gp060_2_6_2mer_model_0.cif

Chain information for fold_goslar_gp219_gp061_gp060_2_6_2mer_model_0.cif #8  
---  
Chain | Description  
A B | .  
C D E F G H | .  
I J | .  
  

> hide #!5 models

> open
> /Users/benjaminadler/Downloads/fold_phikz_gp089full/fold_phikz_gp089full_model_0.cif

Chain information for fold_phikz_gp089full_model_0.cif #9  
---  
Chain | Description  
A | .  
  

> close

> open
> /Users/benjaminadler/Downloads/fold_phikz_gp089full/fold_phikz_gp089full_model_0.cif

Chain information for fold_phikz_gp089full_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> select #1:1-122

922 atoms, 934 bonds, 122 residues, 1 model selected  

> color sel magenta

> select down

922 atoms, 934 bonds, 122 residues, 1 model selected  

> select up

934 atoms, 947 bonds, 123 residues, 1 model selected  

> select #1:156-387

1845 atoms, 1873 bonds, 232 residues, 1 model selected  

> color sel cyan

> open
> /Users/benjaminadler/Downloads/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer/fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif

Chain information for
fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif #2  
---  
Chain | Description  
A B C D E F | .  
  

> mmaker #1 to #2/A

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_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif,
chain A (#2) with fold_phikz_gp089full_model_0.cif, chain A (#1), sequence
alignment score = 595.9  
RMSD between 168 pruned atom pairs is 1.014 angstroms; (across all 349 pairs:
16.722)  
  

> select #2

16890 atoms, 17094 bonds, 2208 residues, 1 model selected  

> hide sel atoms

> select #2/A

2815 atoms, 2849 bonds, 368 residues, 1 model selected  

> show sel cartoons

> select #2/A:116

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/A:115

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

> select #2/A:1-115

880 atoms, 890 bonds, 115 residues, 1 model selected  

> color sel lime

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> select all

19922 atoms, 20177 bonds, 2595 residues, 2 models selected  

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_12mer/fold_goslar_gp061n_12mer_model_0.cif

Chain information for fold_goslar_gp061n_12mer_model_0.cif #3  
---  
Chain | Description  
A B C D E F G H I J K L | .  
  

> close #3

> select #0

Nothing selected  

> hide #2 models

> show #2 models

> save
> /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp089__Goslar_gp061.cxs
> includeMaps true

> close #2

> close

> open
> /Users/benjaminadler/Downloads/fold_phikz_gp129full_portal/fold_phikz_gp129full_portal_model_0.cif

Chain information for fold_phikz_gp129full_portal_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> select #1:1-262

2060 atoms, 2090 bonds, 262 residues, 1 model selected  

> color sel magenta

> select #1:263-896

4985 atoms, 5079 bonds, 634 residues, 1 model selected  

> color sel cyan

> open
> /Users/benjaminadler/Downloads/fold_2024_05_16_20_23_goslar_gp036_5mer/fold_2024_05_16_20_23_goslar_gp036_5mer_model_0.cif

Chain information for fold_2024_05_16_20_23_goslar_gp036_5mer_model_0.cif #2  
---  
Chain | Description  
A B C D E | .  
  

> select #2

38085 atoms, 38730 bonds, 4845 residues, 1 model selected  

> lighting soft

> select all

45130 atoms, 45900 bonds, 5741 residues, 2 models selected  

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> hide sel atoms

> select #2/A

7617 atoms, 7746 bonds, 969 residues, 1 model selected  

> show sel cartoons

> mmaker #2/A 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 fold_phikz_gp129full_portal_model_0.cif, chain A (#1) with
fold_2024_05_16_20_23_goslar_gp036_5mer_model_0.cif, chain A (#2), sequence
alignment score = 1517.2  
RMSD between 324 pruned atom pairs is 1.156 angstroms; (across all 852 pairs:
24.105)  
  

> select #2/A:323

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

> select up

98 atoms, 99 bonds, 11 residues, 1 model selected  
Alignment identifier is 2/A  

> select #2/A:307

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #2/A:307-309

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #2/A:311

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

> select #2/A:311

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

> select #2/A:319

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

> select #2/A:319

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

> select #2/A:363

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

> select #2/A:361-363

22 atoms, 21 bonds, 3 residues, 1 model selected  

> select #2/A:318-319

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #2/A:317-319

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #2/A:313

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

> select #2/A:313-315

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #2/A:319

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

> select #2/A:317-319

24 atoms, 23 bonds, 3 residues, 1 model selected  

> select #2/A:319

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

> select #2/A:1-319

2525 atoms, 2567 bonds, 319 residues, 1 model selected  

> select #2/A:969

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

> select #2/A:320-969

5092 atoms, 5178 bonds, 650 residues, 1 model selected  

> select #2/A:1-319

2525 atoms, 2567 bonds, 319 residues, 1 model selected  

> color sel lime

> select #2/A:320-969

5092 atoms, 5178 bonds, 650 residues, 1 model selected  

> color sel orange

> select #2:1-319

12625 atoms, 12835 bonds, 1595 residues, 1 model selected  

> color sel lime

> select #2:320-969

25460 atoms, 25890 bonds, 3250 residues, 1 model selected  

> color sel orange

> select #2

38085 atoms, 38730 bonds, 4845 residues, 1 model selected  

> show sel cartoons

> select #0

Nothing selected  

> select #1:1-262

2060 atoms, 2090 bonds, 262 residues, 1 model selected  

> color sel magenta

> select #1:263-896

4985 atoms, 5079 bonds, 634 residues, 1 model selected  

> color sel cyan

> select #2:1-319

12625 atoms, 12835 bonds, 1595 residues, 1 model selected  

> color sel lime

> select #2:320-969

25460 atoms, 25890 bonds, 3250 residues, 1 model selected  

> color sel orange

> select #0

Nothing selected  

> hide #1 models

> show #1 models

> save
> /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp129__Goslar_gp036.cxs

> close

> open
> /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp089__Goslar_gp061.cxs
> format session

opened ChimeraX session  

> select ~sel & ##selected

Nothing selected  

> select #2

16890 atoms, 17094 bonds, 2208 residues, 1 model selected  

> show sel cartoons

> select #0

Nothing selected  

> hide #2 models

> show #2 models

> mmaker #1 to #2/F

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_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif,
chain F (#2) with fold_phikz_gp089full_model_0.cif, chain A (#1), sequence
alignment score = 598.9  
RMSD between 167 pruned atom pairs is 1.017 angstroms; (across all 349 pairs:
16.765)  
  

> select #2/F:112

8 atoms, 7 bonds, 1 residue, 1 model selected  
Alignment identifier is 2/F  

> select #2/F:115

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

> select #2/F:113-115

22 atoms, 21 bonds, 3 residues, 1 model selected  

> select #2/F:119

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #2/F:119-120

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #2/F:115

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

> select #2/F:1-115

880 atoms, 890 bonds, 115 residues, 1 model selected  

> hide #1 models

> open
> /Users/benjaminadler/Downloads/fold_phikz_gp089n_gp089c_6_6mer/fold_phikz_gp089n_gp089c_6_6mer_model_0.cif

Chain information for fold_phikz_gp089n_gp089c_6_6mer_model_0.cif #3  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> mmaker #3 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fold_2024_05_30_12_16_goslar_gp061_innerbody_6mer_model_0.cif,
chain F (#2) with fold_phikz_gp089n_gp089c_6_6mer_model_0.cif, chain G (#3),
sequence alignment score = 465.8  
RMSD between 134 pruned atom pairs is 1.033 angstroms; (across all 226 pairs:
6.475)  
  

> hide sel atoms

> select add #2

16890 atoms, 17094 bonds, 2208 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #3

16608 atoms, 16848 bonds, 2124 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> show #1 models

> hide #1 models

> select #3/H

1845 atoms, 1873 bonds, 232 residues, 1 model selected  

> color sel cyan

> hide #3 models

> show #3 models

> select #3

16608 atoms, 16848 bonds, 2124 residues, 1 model selected  

> hide sel cartoons

> select up

16608 atoms, 16848 bonds, 2124 residues, 1 model selected  

> select #3/H

1845 atoms, 1873 bonds, 232 residues, 1 model selected  

> show sel cartoons

> select #2/F:215

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #2/F:215-217

18 atoms, 17 bonds, 3 residues, 1 model selected  

> select #2:215-217

108 atoms, 102 bonds, 18 residues, 1 model selected  

> select #2/F:148

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #2/F:148-150

22 atoms, 21 bonds, 3 residues, 1 model selected  

> open "/Users/benjaminadler/Downloads/fold_phikz_gp092_2mer
> (1)/fold_phikz_gp092_2mer_model_0.cif"

Chain information for fold_phikz_gp092_2mer_model_0.cif #4  
---  
Chain | Description  
A B | .  
  

> close

> open "/Users/benjaminadler/Downloads/fold_phikz_gp092_2mer
> (1)/fold_phikz_gp092_2mer_model_0.cif"

Chain information for fold_phikz_gp092_2mer_model_0.cif #1  
---  
Chain | Description  
A B | .  
  

> select #1:86-440

5782 atoms, 5878 bonds, 710 residues, 1 model selected  

> color sel cyan

> open
> /Users/benjaminadler/Downloads/fold_phikz_gp093full/fold_phikz_gp093full_model_0.cif

Chain information for fold_phikz_gp093full_model_0.cif #2  
---  
Chain | Description  
A | .  
  

> hide #1 models

> close

> open
> /Users/benjaminadler/Downloads/fold_phikz_gp093full/fold_phikz_gp093full_model_0.cif
> format mmcif

Chain information for fold_phikz_gp093full_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp058_6mer/fold_goslar_gp058_6mer_model_0.cif

Chain information for fold_goslar_gp058_6mer_model_0.cif #2  
---  
Chain | Description  
A B C D E F | .  
  

> hide atoms

> show cartoons

> mmaker #1 to #2/A

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_goslar_gp058_6mer_model_0.cif, chain A (#2) with
fold_phikz_gp093full_model_0.cif, chain A (#1), sequence alignment score =
350.9  
RMSD between 40 pruned atom pairs is 0.975 angstroms; (across all 368 pairs:
27.410)  
  

> hide #2 models

> select #1:1-86

649 atoms, 651 bonds, 86 residues, 1 model selected  

> color sel magenta

> select #1:87-440

2692 atoms, 2725 bonds, 349 residues, 1 model selected  

> color sel cyan

> select #1:1-85

641 atoms, 643 bonds, 85 residues, 1 model selected  

> color sel magenta

> select #1:86-440

2700 atoms, 2733 bonds, 350 residues, 1 model selected  

> color sel cyan

> show #2 models

> select #0

Nothing selected  
Alignment identifier is 1/A  
Alignment identifier is 1  

> select #2/A-F:21

30 atoms, 24 bonds, 6 residues, 1 model selected  

> select #2/A-F:21-23

114 atoms, 108 bonds, 18 residues, 1 model selected  

> select #1/A:90

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:90-92

22 atoms, 21 bonds, 3 residues, 1 model selected  

> select #2/A-F:48

42 atoms, 36 bonds, 6 residues, 1 model selected  

> select #2/A-F:48-50

126 atoms, 120 bonds, 18 residues, 1 model selected  

> select #2/A-F:68

30 atoms, 24 bonds, 6 residues, 1 model selected  

> select #2/A-F:68-70

132 atoms, 126 bonds, 18 residues, 1 model selected  

> select #2/A-F:70

54 atoms, 48 bonds, 6 residues, 1 model selected  

> select #2/A-F:70-440

16812 atoms, 17046 bonds, 2226 residues, 1 model selected  

> select #2

19794 atoms, 20064 bonds, 2640 residues, 1 model selected  

> hide sel cartoons

> select #2/A

3299 atoms, 3344 bonds, 440 residues, 1 model selected  

> show sel cartoons

> select #2/A:154

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

539 atoms, 552 bonds, 64 residues, 1 model selected  

> hide #1 models

> select #0

Nothing selected  

> show #1 models

> rainbow

> color bychain

> select #1 color sel white

Expected a keyword  

> select #1

3341 atoms, 3377 bonds, 435 residues, 1 model selected  

> color sel white

> select #2

19794 atoms, 20064 bonds, 2640 residues, 1 model selected  

> rainbow sel

> select #1:86-440

2700 atoms, 2733 bonds, 350 residues, 1 model selected  

> color sel magenta

> select #2/A:112

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

> select up

551 atoms, 552 bonds, 73 residues, 1 model selected  

> select #2/A-F:108

30 atoms, 24 bonds, 6 residues, 1 model selected  

> select #2/A-F:108-110

126 atoms, 120 bonds, 18 residues, 1 model selected  

> select #2/A-F:102

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select #2/A-F:102-104

144 atoms, 138 bonds, 18 residues, 1 model selected  

> select #2/A-F:84

54 atoms, 48 bonds, 6 residues, 1 model selected  

> select #2/A-F:82-84

144 atoms, 138 bonds, 18 residues, 1 model selected  

> select #2/A-F:102

48 atoms, 42 bonds, 6 residues, 1 model selected  

> select #2/A-F:102-104

144 atoms, 138 bonds, 18 residues, 1 model selected  

> select #2/A-F:82

42 atoms, 36 bonds, 6 residues, 1 model selected  

> select #2/A-F:82-84

144 atoms, 138 bonds, 18 residues, 1 model selected  

> select #2/A-F:84

54 atoms, 48 bonds, 6 residues, 1 model selected  

> select #2/A-F:84-91

378 atoms, 372 bonds, 48 residues, 1 model selected  

> select all

23135 atoms, 23441 bonds, 3075 residues, 2 models selected  

> show sel cartoons

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> select #1:1-85

641 atoms, 643 bonds, 85 residues, 1 model selected  

> color sel magenta

> select #1:86-440

2700 atoms, 2733 bonds, 350 residues, 1 model selected  

> color sel cyan

> select #2:1-82

3576 atoms, 3606 bonds, 492 residues, 1 model selected  

> color sel lime

> select #2:83-440

16218 atoms, 16452 bonds, 2148 residues, 1 model selected  

> color sel orange

> select #0

Nothing selected  

> select #2/C:124

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

> select up

142 atoms, 142 bonds, 18 residues, 1 model selected  

> select #2/A-F:123

30 atoms, 24 bonds, 6 residues, 1 model selected  

> select #2/A-F:123-125

138 atoms, 132 bonds, 18 residues, 1 model selected  

> select #2/A-F:146

42 atoms, 42 bonds, 6 residues, 1 model selected  

> select #2/A-F:146-149

198 atoms, 204 bonds, 24 residues, 1 model selected  

> select #2/A-F:139

66 atoms, 66 bonds, 6 residues, 1 model selected  

> select #2/A-F:139

66 atoms, 66 bonds, 6 residues, 1 model selected  

> select #2/A-F:147

36 atoms, 30 bonds, 6 residues, 1 model selected  

> select #2/A-F:147-149

156 atoms, 156 bonds, 18 residues, 1 model selected  

> select #0

Nothing selected  

> save
> /Users/benjaminadler/Desktop/Proteolysis_compare__PHIKZ_gp093__Goslar_gp058.cxs

> close #1

> close

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_6_6mer_v2/fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif

Chain information for fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif #1  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_6_6mer_v2/fold_goslar_gp061n_gp061c_6_6mer_v2_model_1.cif

Chain information for fold_goslar_gp061n_gp061c_6_6mer_v2_model_1.cif #2  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_6_6mer_v2/fold_goslar_gp061n_gp061c_6_6mer_v2_model_2.cif

Chain information for fold_goslar_gp061n_gp061c_6_6mer_v2_model_2.cif #3  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> mmaker #3 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 fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif, chain I (#1) with
fold_goslar_gp061n_gp061c_6_6mer_v2_model_2.cif, chain G (#3), sequence
alignment score = 1059.2  
RMSD between 144 pruned atom pairs is 0.571 angstroms; (across all 219 pairs:
5.640)  
  

> mmaker #2 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 fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif, chain I (#1) with
fold_goslar_gp061n_gp061c_6_6mer_v2_model_1.cif, chain G (#2), sequence
alignment score = 1071.2  
RMSD between 141 pruned atom pairs is 0.743 angstroms; (across all 219 pairs:
3.312)  
  

> hide #2 models

> hide #3 models

> hide #1 models

> show #2 models

> hide #2 models

> show #3 models

> show #1 models

> hide #3 models

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061_gp060_6_6mer/fold_goslar_gp061_gp060_6_6mer_model_0.cif

Chain information for fold_goslar_gp061_gp060_6_6mer_model_0.cif #4  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
  

> hide #1 models

> show #4 cartoons

> hide #4 atoms

> color bfactor #4

31236 atoms, 4008 residues, atom bfactor range 15.6 to 89.6  

> coulombic #4

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_A SES surface
#4.1: minimum, -16.78, mean -0.14, maximum 12.28  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_B SES surface
#4.2: minimum, -16.38, mean -0.14, maximum 12.37  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_C SES surface
#4.3: minimum, -14.95, mean -0.16, maximum 12.36  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_D SES surface
#4.4: minimum, -15.34, mean -0.14, maximum 12.45  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_E SES surface
#4.5: minimum, -15.92, mean -0.13, maximum 12.50  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_F SES surface
#4.6: minimum, -19.73, mean -0.14, maximum 12.40  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_G SES surface
#4.7: minimum, -22.91, mean -1.62, maximum 15.80  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_H SES surface
#4.8: minimum, -18.42, mean -1.59, maximum 14.82  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_I SES surface
#4.9: minimum, -18.39, mean -1.57, maximum 12.68  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_J SES surface
#4.10: minimum, -18.95, mean -1.63, maximum 15.49  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_K SES surface
#4.11: minimum, -18.43, mean -1.60, maximum 13.82  
Coulombic values for fold_goslar_gp061_gp060_6_6mer_model_0.cif_L SES surface
#4.12: minimum, -19.73, mean -1.60, maximum 13.45  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color #!4 bychain

> show #1 models

> hide #1 models

> show #3 models

> hide #3 models

> show #1 models

> mmaker #4 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 fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif, chain I (#1) with
fold_goslar_gp061_gp060_6_6mer_model_0.cif, chain B (#4), sequence alignment
score = 990.2  
RMSD between 99 pruned atom pairs is 0.561 angstroms; (across all 219 pairs:
17.222)  
  

> hide #1 models

> hide #!4 models

> show #1 models

> ui mousemode right distance

> distance #1/C:4@CB #1/F:4@CB

Distance between fold_goslar_gp061n_gp061c_6_6mer_v2_model_0.cif #1/C SER 4 CB
and /F SER 4 CB: 29.757Å  

> close

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif

Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif #1  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> color bychain

> hide atoms

> show cartoons

> color bfactor

29754 atoms, 3804 residues, atom bfactor range 14.6 to 87.5  

> color bychain

> show surfaces

> select #1A,B,C,D,E,F

Expected an objects specifier or a keyword  

> select #1/A,B,C,D,E,F

5286 atoms, 5346 bonds, 690 residues, 1 model selected  

> color sel purple

> select #1/G,H,I,J,K,L

10122 atoms, 10248 bonds, 1314 residues, 1 model selected  

> color sel magenta

> select #1/K,L,M,N,O,P

12938 atoms, 13136 bonds, 1638 residues, 1 model selected  

> color sel red

> select up

29754 atoms, 30174 bonds, 3804 residues, 7 models selected  

> select up

29754 atoms, 30174 bonds, 3804 residues, 19 models selected  

> select #1/G,H,I,J,K,L

10122 atoms, 10248 bonds, 1314 residues, 1 model selected  

> color sel magenta

> select #1/M,N,O,P,Q,R

14346 atoms, 14580 bonds, 1800 residues, 1 model selected  

> COLOR SEL RED

Unknown command: COLOR SEL RED  

> color sel red

> lighting soft

> select #0

Nothing selected  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif

Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif #2  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif

Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif #3  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> hide #!1 models

> hide #3 models

> show #3 models

> show #!1 models

> mmaker #3 to #1


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

Log:
Startup Messages  
---  
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle  
Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with
that from NMRSTAR bundle  
  

> lighting soft

> graphics silhouettes true

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif

Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_0.cif #1  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif

Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_1.cif #2  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  

> open
> /Users/benjaminadler/Downloads/fold_goslar_gp061n_gp061c_gp060_6_6_6mer/fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif

Chain information for fold_goslar_gp061n_gp061c_gp060_6_6_6mer_model_2.cif #3  
---  
Chain | Description  
A B C D E F | .  
G H I J K L | .  
M N O P Q R | .  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: MNWA3LL/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5 (22G74)
      Kernel Version: Darwin 22.6.0
      Time since boot: 11 days, 6 hours, 30 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    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: 2.10.5
    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: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    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: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    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
    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: 1.1.8
    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: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    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-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    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
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    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: 1.33.3
    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: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    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: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 15 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 in garbage collection

comment:2 by Eric Pettersen, 15 months ago

Resolution: → duplicate
Status: accepted → closed
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