Opened 13 months ago

Closed 13 months ago

#15999 closed defect (duplicate)

Crash in garbage collection

Reported by: chimerax-bug-report@… Owned by: pett
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-14.5-x86_64-i386-64bit
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 0x0000000321b61000 (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 0x0000000320b5e000 (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 0x000000031fb5b000 (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 0x000000031eb58000 (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 0x000000031db55000 (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 0x000000031cb52000 (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 0x000000031bb4f000 (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 0x000000031ab4c000 (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 0x0000000319b49000 (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 0x0000000318b46000 (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 0x0000000317b43000 (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 0x000000020466b240 (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/atomic/molarray.py", line 161 in 
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
  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 2499 in _parse_arg
  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 2640 in _process_positional_arguments
  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 2864 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.surface._surface, chimerax.pdb_lib._load_libs, 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.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, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56)


{"app_name":"ChimeraX","timestamp":"2024-09-23 14:53:56.00 -0500","app_version":"1.7.1","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","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 14.5 (23F79)","roots_installed":0,"name":"ChimeraX","incident_id":"35A0818C-1D94-44A4-BBDA-095AF6A93DD4"}
{
  "uptime" : 2900000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookAir10,1",
  "coalitionID" : 301515,
  "osVersion" : {
    "train" : "macOS 14.5",
    "build" : "23F79",
    "releaseType" : "User"
  },
  "captureTime" : "2024-09-23 14:53:48.7351 -0500",
  "codeSigningMonitor" : 1,
  "incident" : "35A0818C-1D94-44A4-BBDA-095AF6A93DD4",
  "pid" : 52648,
  "translated" : true,
  "cpuType" : "X86-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-09-05 15:58:49.8448 -0500",
  "procStartAbsTime" : 58114853879919,
  "procExitAbsTime" : 71409449325015,
  "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":"57A90D80-F304-5878-AA3D-33EE15DFFA9E","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "C26E1A6D-208C-0431-BC9F-D1252B1481C3",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "wakeTime" : 3326,
  "sleepWakeUUID" : "DA464BDF-2419-4402-9470-768334AAD564",
  "sip" : "enabled",
  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 4366069591\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1043cf000-1043d3000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
  "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":52648},
  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 4366069591\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      __TEXT                      1043cf000-1043d3000    [   16K] r-x\/r-x SM=COW  \/Applications\/ChimeraX-1.7.1.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" : 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  "reportNotes" : [
  "PC register does not match crashing frame (0x0 vs 0x7FF8A869EA78)"
]
}
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
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/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif

Chain information for fold_2024_08_23_12_59_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> set bgColor white

> graphics silhouettes true

> open 7fbi

Summary of feedback from opening 7fbi fetched from pdb  
---  
note | Fetching compressed mmCIF 7fbi from
http://files.rcsb.org/download/7fbi.cif  
  
7fbi title:  
Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5 [more info...]  
  
Chain information for 7fbi #2  
---  
Chain | Description | UniProt  
A | Envelope glycoprotein B | R4R670_EBVG 22-674  
H | 3A3 heavy chain |  
L | 3A3 light chain |  
M | 3A5 light chain |  
N | 3A5 heavy chain |  
  

> select add #2

7777 atoms, 7940 bonds, 3 pseudobonds, 1005 residues, 2 models selected  

> show sel cartoons

> hide sel atoms

> mmaker #2 to #!

> matchmaker #2 to #!

Invalid "to" argument: invalid atoms specifier  

> 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_2024_08_23_12_59_model_0.cif, chain A (#1) with 7fbi, chain A
(#2), sequence alignment score = 1187.8  
RMSD between 194 pruned atom pairs is 1.238 angstroms; (across all 548 pairs:
4.367)  
  

> ui mousemode right select

> select clear

> select #2/A:160

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

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select clear

> select #2/A:538

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

> select #2/A:538-539

19 atoms, 18 bonds, 2 residues, 1 model selected  

> select #2/A:112

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

> select #2/A:112-113

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #1/A:129

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

> select #1/A:128

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

> select #1/A:129

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

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif

Chain information for fold_2024_09_02_11_52_model_0.cif #3  
---  
Chain | Description  
A B C | .  
  

> select down

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

> select ~sel & ##selected

19823 atoms, 20247 bonds, 2534 residues, 1 model selected  

> select ~sel & ##selected

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

> 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_2024_08_23_12_59_model_0.cif, chain A (#1) with
fold_2024_09_02_11_52_model_0.cif, chain A (#3), sequence alignment score =
1481.2  
RMSD between 357 pruned atom pairs is 1.205 angstroms; (across all 770 pairs:
19.068)  
  

> hide #1 models

> select add #1

19830 atoms, 20253 bonds, 2535 residues, 1 model selected  

> color #2 #919191ff

> select #2/A:112

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

> select #2/A:112-113

21 atoms, 21 bonds, 2 residues, 1 model selected  

> show #1 models

> hide #3 models

> select #1/A:209

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

> select #1/A:213

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

> select #1/A:212

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show #3 models

> select #3/A:103

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/C:154

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

> select #3/A:185

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

> select #3/A:186

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

> select #3/A:187

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

> select #3/A:188

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

> select #3/A:185

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

> select #3/A:186

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

> select #3/A:187

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

> hide #3 models

> select add #3

19677 atoms, 20088 bonds, 2490 residues, 1 model selected  

> hide #!2 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B #1/C

Alignment identifier is 1  

> select #1/A-C:52-56

99 atoms, 96 bonds, 15 residues, 1 model selected  

> select #1/A-C:1-56

1173 atoms, 1197 bonds, 168 residues, 1 model selected  

> select #1/A-C:1-56

1173 atoms, 1197 bonds, 168 residues, 1 model selected  

> select #1/A-C:1-56

1173 atoms, 1197 bonds, 168 residues, 1 model selected  

> select #1/A-C:57

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

> select #1/A-C:1-57

1194 atoms, 1221 bonds, 171 residues, 1 model selected  

> open 5ㅊㅌㄹ

Traceback (most recent call last):  
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  
cmd.run(cmd_text)  
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  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
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  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 166, in provider_open  
models, status = collated_open(session, database_name, ident,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/mmcif/__init__.py", line 108, in fetch  
return fetcher(session, ident, ignore_cache=ignore_cache, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "src/mmcif.pyx", line 426, in chimerax.mmcif.mmcif.fetch_mmcif  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/fetch.py", line 99, in fetch_file  
retrieve_url(url, filename, uncompress=uncompress,
transmit_compressed=transmit_compressed,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/fetch.py", line 192, in retrieve_url  
with urlopen(request, timeout=timeout, context=ssl_context) as response:  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 216, in urlopen  
return opener.open(url, data, timeout)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 519, in open  
response = self._open(req, data)  
^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 536, in _open  
result = self._call_chain(self.handle_open, protocol, protocol +  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 496, in _call_chain  
result = func(*args)  
^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1377, in http_open  
return self.do_open(http.client.HTTPConnection, req)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py",
line 1348, in do_open  
h.request(req.get_method(), req.selector, req.data, headers,  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1282, in request  
self._send_request(method, url, body, headers, encode_chunked)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1293, in _send_request  
self.putrequest(method, url, **skips)  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1131, in putrequest  
self._output(self._encode_request(request))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1211, in _encode_request  
return request.encode('ascii')  
^^^^^^^^^^^^^^^^^^^^^^^  
UnicodeEncodeError: 'ascii' codec can't encode characters in position 15-17:
ordinal not in range(128)  
  
UnicodeEncodeError: 'ascii' codec can't encode characters in position 15-17:
ordinal not in range(128)  
  
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py",
line 1211, in _encode_request  
return request.encode('ascii')  
^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open 5cxf

5cxf title:  
Crystal structure of the extracellular domain of glycoprotein B from Human
Cytomegalovirus [more info...]  
  
Chain information for 5cxf #4  
---  
Chain | Description | UniProt  
A B C | Envelope glycoprotein B | GB_HCMVA 78-706  
  
Non-standard residues in 5cxf #4  
---  
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)  
CA — calcium ion  
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> 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_2024_08_23_12_59_model_0.cif, chain A (#1) with 5cxf, chain B
(#4), sequence alignment score = 1185.8  
RMSD between 314 pruned atom pairs is 1.313 angstroms; (across all 565 pairs:
3.066)  
  

> select clear

> select #4/C:240

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

> select #4/C:156

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

> select #4/C:157

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

> select #4/C:156

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

> select #4/C:157

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

> select #4/C:156

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

> select #4/C:157

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

> select clear

> select #4/C:156

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

> select #4/C:157

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

> select #4/C:156

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

> select clear

> select #4/C:157

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

> select #4/C:156

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

> select #4/C:157

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

> select #4/C:156

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

> select #4/C:240

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

> select clear

> select #4/C:239

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

> select #4/C:240

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

> select #4/C:238

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

> select #4/C:239

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

> select clear

> select #4/C:238

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

> select #4/C:239

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

> select #4/C:240

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

> select #4/C:241

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

> select #4/C:240

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

> select #4/C:239

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

> select #4/C:238

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

> select #4/C:239

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

> select #4/C:240

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

> select #4/C:239

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

> select #4/C:240

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

> select #4/C:239

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

> select #4/C:240

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

> select #4/C:239

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

> show #3 models

> hide #!4 models

> select add #4

14373 atoms, 14732 bonds, 12 pseudobonds, 1749 residues, 3 models selected  

> select #3/A:186

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

> select #3/A:187

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

> select #3/A:103

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:102

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

> select #3/A:103

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #3/A:102

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

> select #3/A:186

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

> select #3/A:187

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

> select #3/A:186

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

> select #3/A:187

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

> select #1/A:129

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

> show #!2 models

> hide #3 models

> select #1/A:130

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

> select #1/A:131

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

> select #1/A:211

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

> select #1/A:212

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:213

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

> select clear

> select #1/A:212

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/A:213

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

> select #1/A:214

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

> show #!4 models

> select #4/B:242

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

> select #1/A:213

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

> hide #1 models

> hide #!2 models

> show #1 models

> select add #1

19830 atoms, 20253 bonds, 2535 residues, 1 model selected  

> color #4 #d4fb79ff

> select clear

> select #1/A:213

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

> select #1/A:214

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

> select #1/A:213

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

> select #1/A:214

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

> select #4/B:242

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

> select #4/B:241

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

> select #4/B:241

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

> select #4/B:240

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

> select #4/B:239

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

> select #4/B:240

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

> select #4/B:241

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

> select #1/A:213

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

> select #1/A:214

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

> select #4/B:241

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

> select #4/B:240

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

> select clear

> select #4/B:243

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

> select clear

> select #4/B:241

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

> select #4/B:240

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

> select clear

> select #4/B:241

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

> select #4/B:239

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

> select #4/B:240

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

> select #4/B:239

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

> select #4/B:238

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

> select #4/B:240

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

> select #1/A:701

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> select #4/B:241

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

> open 5c6t

5c6t title:  
Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab [more
info...]  
  
Chain information for 5c6t #5  
---  
Chain | Description | UniProt  
A | Envelope glycoprotein B | GB_HCMVT 87-698  
H | 1G2 Fab heavy chain |  
L | 1G2 Fab light chain |  
  
Non-standard residues in 5c6t #5  
---  
MG — magnesium ion  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
5c6t mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> hide #!4 models

> select add #4

14373 atoms, 14732 bonds, 12 pseudobonds, 1749 residues, 3 models selected  

> mmaker $5 to $1

> matchmaker $5 to $1

Missing or invalid "matchAtoms" argument: invalid atoms specifier  

> 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_2024_08_23_12_59_model_0.cif, chain A (#1) with 5c6t, chain A
(#5), sequence alignment score = 1048.8  
RMSD between 231 pruned atom pairs is 1.238 angstroms; (across all 557 pairs:
7.840)  
  

> select #5/A:242

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

> select #1/C:696

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

> select #5/A:241

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

> select #5/A:240

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

> select clear

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif

Chain information for fold_2024_08_23_12_59_model_0.cif #6  
---  
Chain | Description  
A B C | .  
  

> hide #!5 models

> hide #6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #1/A #1/B #1/C #6/A #6/B #6/C

Alignment identifier is 1  

> select #1/A-C:1 #6/A-C:1

48 atoms, 42 bonds, 6 residues, 2 models selected  

> select #1/A-C:1-477 #6/A-C:1-477

22110 atoms, 22662 bonds, 2862 residues, 2 models selected  
. [ID: 1] region 6 chains [1-477] RMSD: 0.000  
  

> select clear

> select #1/A-C:1-2 #6/A-C:1-2

90 atoms, 84 bonds, 12 residues, 2 models selected  

> select #1/A-C #6/A-C

39660 atoms, 40506 bonds, 5070 residues, 2 models selected  
. [ID: 1] region 6 chains [1-845] RMSD: 0.000  
  

> select clear

> select #1/C:680

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

> select #1/C:674

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

> select #1/C:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/C:674

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

> select #1/C:680

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

> select #1/C:682

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

> select #1/C:683

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

> select #1/C:684

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

> select add #1/C:680

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

> select #1/C:672

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

> select #1/C:670

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

> select clear

> select #1/C:671

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

> select #1/C:672

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

> select #1/C:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #1/C:674

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

> select #1/C:675

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

> select #1/C:676

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

> select #1/C:677

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

> select #1/C:678

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

> select #1/C:679

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

> select #1/C:680

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

> select #1/C:670

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

> select clear

> select #1/C:671

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

> select #1/C:672

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

> select #1/C:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select clear

> show #6 models

> show #3 models

> hide #6 models

> hide #3 models

> show #3 models

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_ECD_FD/fold_2024_08_23_17_18_model_0.cif

Chain information for fold_2024_08_23_17_18_model_0.cif #7  
---  
Chain | Description  
A B C | .  
  

> hide #3 models

> hide #1 models

> select #7/C:640

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

> show sel atoms

> select #7/C:644

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

> show sel atoms

> select #7/B:240

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

> select add #7/B:241

12 atoms, 10 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #7/C:654

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

> select add #7/C:653

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

> show sel atoms

> select #7/B:241

4 atoms, 3 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #7/C:640

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

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif

Chain information for fold_2024_08_23_12_59_model_0.cif #8  
---  
Chain | Description  
A B C | .  
  

> hide #8 models

> hide #7 models

> show #8 models

> select #8/B:685

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

> select #8/B:678

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

> select #8/B:672

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

> select #8/B:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/B:657

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

> select #8/B:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/B:657

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

> select #8/B:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/B:657

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

> select #8/B:661

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

> select #8/B:666

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

> select #8/B:665

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

> select #8/B:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/B:668

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

> select #8/B:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/B:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/B:669

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

> select #8/C:699

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

> select #8/C:698

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

> select add #8/C:697

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add #8/C:694

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select add #8/C:693

26 atoms, 22 bonds, 4 residues, 1 model selected  

> select add #8/C:692

34 atoms, 29 bonds, 5 residues, 1 model selected  

> show sel atoms

> select #8/C:690

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

> select #8/C:690

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

> select add #8/C:689

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

> show sel atoms

> select #8/C:689

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

> select #8/C:689

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

> select #8/C:686

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

> show sel atoms

> show #!4 models

> select #8/C:670

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

> select #8/C:670

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

> select #8/C:670

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

> select #8/C:671

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

> select #8/C:672

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

> select #8/C:671

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

> select #8/C:674

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

> select #8/C:673

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select #8/C:672

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

> select #8/C:671

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

> select #8/C:671

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

> select #8/C:670

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

> select #8/C:669

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

> select #8/C:669

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

> select #8/C:669

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

> select #8/C:669

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

> select #8/C:668

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

> select #8/C:667

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

> select #8/C:667

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

> select #8/C:666

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

> select #8/C:665

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

> select #8/C:664

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

> select #8/C:663

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

> select #8/C:662

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

> open 3fvc

Summary of feedback from opening 3fvc fetched from pdb  
---  
note | Fetching compressed mmCIF 3fvc from
http://files.rcsb.org/download/3fvc.cif  
  
3fvc title:  
Crystal structure of a trimeric variant of the Epstein-Barr virus glycoprotein
B [more info...]  
  
Chain information for 3fvc #9  
---  
Chain | Description | UniProt  
A | Glycoprotein GP110 | VGLB_EBV 23-685  
  
Non-standard residues in 3fvc #9  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3fvc mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> 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_2024_08_23_12_59_model_0.cif, chain A (#1) with
fold_2024_09_02_11_52_model_0.cif, chain A (#3), sequence alignment score =
1481.2  
RMSD between 357 pruned atom pairs is 1.205 angstroms; (across all 770 pairs:
19.068)  
  

> mmaker #9 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_2024_08_23_12_59_model_0.cif, chain A (#1) with 3fvc, chain A
(#9), sequence alignment score = 1612.8  
RMSD between 319 pruned atom pairs is 0.942 angstroms; (across all 554 pairs:
3.871)  
  

> select #9/A:679

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

> hide #!4 models

> select #8/A:659

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

> select #8/A:666

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

> select #8/A:667

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

> select #9/A:679

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

> select #8/A:681

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

> select #8/A:678

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

> select #8/A:679

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

> select #8/A:680

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

> select #9/A:679

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

> select #9/A:679

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

> select #8/A:666

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

> select #8/C:201

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

> select add #8/C:202

14 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #8/B:266

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

> select add #8/B:267

12 atoms, 10 bonds, 2 residues, 1 model selected  

> show sel atoms

> select #8/A:678

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

> select #8/A:692

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

> select #8/A:685

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

> select #8/A:680

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

> select #8/C:32

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

> select #8/C:415

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

> select #9/A:655

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

> select #9/A:654

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

> select #8/A:655

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

> select #9/A:655

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

> close

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif

Chain information for fold_2024_08_23_12_59_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> save /Users/kjyeol/Desktop/KSHV_gB_FL_AF3_prediction.pdb relModel #1

> select /B:662

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

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif

Chain information for fold_2024_09_02_11_52_model_0.cif #2  
---  
Chain | Description  
A B C | .  
  

> 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_2024_08_23_12_59_model_0.cif, chain A (#1) with
fold_2024_09_02_11_52_model_0.cif, chain A (#2), sequence alignment score =
1481.2  
RMSD between 357 pruned atom pairs is 1.205 angstroms; (across all 770 pairs:
19.068)  
  

> hide #1 models

> select add #1

19830 atoms, 20253 bonds, 2535 residues, 1 model selected  

> select #2/C:27

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

> select #2/C:20

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

> select #2/C:21

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

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A #2/B #2/C

Alignment identifier is 1  

> select #2/A-C:1

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

> select #2/A-C:1-19

444 atoms, 447 bonds, 57 residues, 1 model selected  

> select #2/A-C:1-19

444 atoms, 447 bonds, 57 residues, 1 model selected  

> select #2/A-C:22

18 atoms, 15 bonds, 3 residues, 1 model selected  

> select #2/A-C:1-22

522 atoms, 528 bonds, 66 residues, 1 model selected  

> close

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/HHV7/AF3/HHV7gB_FL_Trimer/fold_2024_07_24_17_59_model_0.cif

Chain information for fold_2024_07_24_17_59_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  

> open /Users/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif

Chain information for fold_2024_09_02_11_52_model_0.cif #2  
---  
Chain | Description  
A B C | .  
  

> mmaker #2 to #1


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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/kjyeol/Library/CloudStorage/Box-
> Box/JeongRyeolKim/project/SHIELD_ARPA-
> H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif

Chain information for fold_2024_09_02_11_52_model_0.cif #1  
---  
Chain | Description  
A B C | .  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M1
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 Air
      Model Identifier: MacBookAir10,1
      Model Number: MGN63KH/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.121.1
      OS Loader Version: 10151.121.1

Software:

    System Software Overview:

      System Version: macOS 14.5 (23F79)
      Kernel Version: Darwin 23.5.0
      Time since boot: 90 days, 1 hour, 26 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 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 pett, 13 months ago

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

comment:2 by pett, 13 months ago

Resolution: → duplicate
Status: accepted → closed
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