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Opened 18 months ago
Closed 18 months ago
#15268 closed defect (duplicate)
Crash in garbage collection
| Reported by: | 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-14.4.1-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 0x000070000d94c000 (most recent call first):
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 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 0x00007ff84d2d0100 (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/grako/ast.py", line 63 in update
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 19 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 90 in copy
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 642 in _try
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 665 in _option
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
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 371 in _residue_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 359 in block7
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
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 361 in _chain_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 323 in block0
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
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 325 in _model_parts_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 200 in _model_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 157 in block0
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 787 in _positive_closure
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 159 in _model_list_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 136 in _as_term_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 89 in _atom_specifier_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
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 93 in _atom_specifier_
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 497 in _invoke_rule
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 458 in _call
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 59 in wrapper
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 206 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/atomspec.py", line 192 in _parse_unquoted
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 121 in parse
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/defattr.py", line 180 in defattr
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 81 in add_standard_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/charge.py", line 34 in add_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 110 in assign_charges
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
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/run.py", line 49 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 525 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
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.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.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 59)
{"app_name":"ChimeraX","timestamp":"2024-05-21 22:19:48.00 +0100","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 14.4.1 (23E224)","roots_installed":0,"name":"ChimeraX","incident_id":"86DB3C35-BEF5-4595-AB6C-018868671A69"}
{
"uptime" : 1800,
"procRole" : "Foreground",
"version" : 2,
"userID" : 1128307364,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 881,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-05-21 22:19:39.1386 +0100",
"codeSigningMonitor" : 0,
"incident" : "86DB3C35-BEF5-4595-AB6C-018868671A69",
"pid" : 944,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-05-21 21:49:40.2839 +0100",
"procStartAbsTime" : 85689975144,
"procExitAbsTime" : 1884565401495,
"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":"17423086-4649-5655-8652-0ADDB9D62739","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D4945465-AD9F-9A5A-197B-8F817ADA25CA",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4503146327\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10c689000-10c68d000 [ 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":944},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4503146327\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10c689000-10c68d000 [ 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},
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===== 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 /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi-
> AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb
Summary of feedback from opening
/Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi-
AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK --------------------- added by autoBUSTER
-------------------------------
Ignored bad PDB record found on line 3
REMARK run at = Mon May 20 16:22:27 BST 2024
Ignored bad PDB record found on line 13
REMARK Files used:
Ignored bad PDB record found on line 14
REMARK PDB = buster05/pdbchk.pdb
Ignored bad PDB record found on line 15
REMARK MTZ = buster05/mtzchk.mtz
49 messages similar to the above omitted
Chain information for Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #1
---
Chain | Description
A | No description available
> open
> /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo-
> structure.pdb
Summary of feedback from opening
/Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo-
structure.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK --------------------- added by autoBUSTER
-------------------------------
Ignored bad PDB record found on line 3
REMARK run at = Thu Jan 11 16:00:30 GMT 2024
Ignored bad PDB record found on line 12
REMARK Files used:
Ignored bad PDB record found on line 13
REMARK PDB = buster11/pdbchk.pdb
Ignored bad PDB record found on line 14
REMARK MTZ = /data/rds/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL
109 messages similar to the above omitted
Chain information for BCL6_apo-structure.pdb #2
---
Chain | Description
A | No description available
> close
> open
> /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo-
> structure.pdb format pdb
Summary of feedback from opening
/Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL6_13/BCL6_apo-
structure.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK --------------------- added by autoBUSTER
-------------------------------
Ignored bad PDB record found on line 3
REMARK run at = Thu Jan 11 16:00:30 GMT 2024
Ignored bad PDB record found on line 12
REMARK Files used:
Ignored bad PDB record found on line 13
REMARK PDB = buster11/pdbchk.pdb
Ignored bad PDB record found on line 14
REMARK MTZ = /data/rds/HDSD_Work/jwiebe/BCL6/231206_mx34334-7/BCL
109 messages similar to the above omitted
Chain information for BCL6_apo-structure.pdb #1
---
Chain | Description
A | No description available
> open /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi-
> AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb
Summary of feedback from opening
/Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240502_VMXI/VMXi-
AB2883_47x/Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK --------------------- added by autoBUSTER
-------------------------------
Ignored bad PDB record found on line 3
REMARK run at = Mon May 20 16:22:27 BST 2024
Ignored bad PDB record found on line 13
REMARK Files used:
Ignored bad PDB record found on line 14
REMARK PDB = buster05/pdbchk.pdb
Ignored bad PDB record found on line 15
REMARK MTZ = buster05/mtzchk.mtz
49 messages similar to the above omitted
Chain information for Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2
---
Chain | Description
A | No description available
> ui tool show Distances
> matchmaker
Missing or invalid "matchAtoms" argument: empty atom specifier
> matchmaker /A /B
Missing required "to" argument
> matchmaker #1 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 Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb, chain A (#2)
with BCL6_apo-structure.pdb, chain A (#1), sequence alignment score = 656.4
RMSD between 130 pruned atom pairs is 0.348 angstroms; (across all 131 pairs:
0.408)
> hide atoms
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> select add #1
1195 atoms, 1044 bonds, 298 residues, 1 model selected
> select add #2
2237 atoms, 2064 bonds, 467 residues, 2 models selected
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> preset "overall look" "publication 2 (depth-cued)"
Using preset: Overall Look / Publication 2 (Depth-Cued)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes f
lighting depthCue t
> ui tool show "Color Actions"
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
BCL6_apo-structure.pdb #1/A LEU 0
BCL6_apo-structure.pdb #1/A ARG 13
BCL6_apo-structure.pdb #1/A ARG 28
BCL6_apo-structure.pdb #1/A GLN 64
BCL6_apo-structure.pdb #1/A GLU 77
BCL6_apo-structure.pdb #1/A ARG 98
BCL6_apo-structure.pdb #1/A GLU 115
BCL6_apo-structure.pdb #1/A LYS 123
BCL6_apo-structure.pdb #1/A LYS 126
BCL6_apo-structure.pdb #1/A GLU 129
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A SER 7
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ILE 9
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 13
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 28
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 40
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 44
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLN 64
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A LEU 65
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 81
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 94
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 98
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 99
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 115
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ARG 122
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A LYS 123
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A ILE 125
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A LYS 126
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A SER 128
Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb #2/A GLU 129
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for BCL6_apo-structure.pdb_A SES surface #1.1: minimum,
-10.04, mean -0.53, maximum 9.43
Coulombic values for Flag-BCL6_apo_VMXi2883_47x_buster05-corrected.pdb_A SES
surface #2.1: minimum, -15.18, mean -1.32, maximum 8.26
To also show corresponding color key, enter the above coulombic command and
add key true
> transparency /A 50
> transparency /B 50
> transparency /B 70
> transparency /A 70
> transparency /A 90
> select subtract #1
1042 atoms, 1020 bonds, 169 residues, 3 models selected
> select subtract #2
1 model selected
> transparency /A 70
> close #2
> close
> open
> /Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240206_mx34334-11/BCL6_CCT368763_2/BCL6_CCT368763_2_buster12.2-YV-
> final.pdb format pdb
Summary of feedback from opening
/Volumes/DATA/DCT/UCCT/HITDISSD/HDSD_Work/jwiebe/BCL6/240206_mx34334-11/BCL6_CCT368763_2/BCL6_CCT368763_2_buster12.2-YV-
final.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK --------------------- added by autoBUSTER
-------------------------------
Ignored bad PDB record found on line 3
REMARK run at = Wed Mar 6 15:12:54 GMT 2024
Ignored bad PDB record found on line 14
REMARK Files used:
Ignored bad PDB record found on line 15
REMARK PDB = buster12.2-YV_fixed/pdbchk.pdb
Ignored bad PDB record found on line 16
REMARK MTZ = /data/rds/HDSD_Work/jwiebe/BCL6/240206_mx34334-11/BC
119 messages similar to the above omitted
Chain information for BCL6_CCT368763_2_buster12.2-YV-final.pdb #1
---
Chain | Description
A | No description available
Drag select of 2 residues
> hide sel atoms
> select add #1
1226 atoms, 1082 bonds, 294 residues, 1 model selected
> hide sel atoms
> select ::name="763"
19 atoms, 21 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1
1226 atoms, 1082 bonds, 294 residues, 1 model selected
> color sel light sea green
> color sel light gray
> color sel forest green
> color sel orange
> color sel orange red
> color sel hot pink
> ui tool show "Color Actions"
> color sel cornflower blue
> color sel light sea green
> color sel cornflower blue
> color sel dark red
> color sel maroon
> color sel crimson
> color sel orange red
> color sel crimson
> color sel cornflower blue
> select ::name="763"
19 atoms, 21 bonds, 1 residue, 1 model selected
> color sel byhetero
> ui tool show "Crystal Contacts"
> ui tool show "Unit Cell"
> unitcell #1
> select add #2.1
1245 atoms, 1103 bonds, 295 residues, 2 models selected
> close #2.1
> select add #2.2
1245 atoms, 1103 bonds, 295 residues, 2 models selected
> select add #2.8
2471 atoms, 2185 bonds, 589 residues, 3 models selected
> select add #2.7
3697 atoms, 3267 bonds, 883 residues, 4 models selected
> select add #2.6
4923 atoms, 4349 bonds, 1177 residues, 5 models selected
> close #2.7
> select add #2.4
4923 atoms, 4349 bonds, 1177 residues, 5 models selected
> select add #2.5
6149 atoms, 5431 bonds, 1471 residues, 6 models selected
> select add #2.3
7375 atoms, 6513 bonds, 1765 residues, 7 models selected
> close #2.3
> close #2.2
> close #2.4
> close #2.5
> close #2.11
> close #2.10
> close #2.9
> close #2.8
> close #2.6
> select add #2.12
1245 atoms, 1103 bonds, 295 residues, 2 models selected
> color sel dark gray
> select ::name="763"
38 atoms, 42 bonds, 2 residues, 2 models selected
> color #1/A 763 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A 763 201 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A 763 201 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A 201 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #1/A 201 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> select clear
> select up
Nothing selected
> select #1/A:201@C3
1 atom, 1 residue, 1 model selected
> select add ::name="763"
38 atoms, 42 bonds, 2 residues, 2 models selected
> color green #1/A 201
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /A 201 green
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color sel cornflower blue
> color sel byhetero
Drag select of 3 residues
> select
2452 atoms, 2164 bonds, 588 residues, 3 models selected
> select add #1/A#2.12/A
2452 atoms, 2164 bonds, 588 residues, 3 models selected
> coulombic sel
The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:
BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A ASN -1
BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A LEU 0
BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A GLN 64
BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A ARG 98
BCL6_CCT368763_2_buster12.2-YV-final.pdb #1/A LYS 126
BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A ASN -1
BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A LEU 0
BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A GLN 64
BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A ARG 98
BCL6_CCT368763_2_buster12.2-YV-final.pdb #12 #2.12/A LYS 126
===== Log before crash end =====
Log:
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
OpenGL version: 4.1 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
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: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 32 minutes, 12 seconds
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
C27F390:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: HTQJ401719
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
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-Clipper: 0.22.4
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 , 18 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 18 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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