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Opened 21 months ago
Closed 21 months ago
#14407 closed defect (can't reproduce)
Crash in garbage collection while parsing atom spec
| Reported by: | 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-14.0-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x0000000319d63000 (most recent call first):
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x0000000205288240 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 52 in
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 52 in iteritems
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 55 in items
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/ast.py", line 92 in copy
File "/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/grako/contexts.py", line 679 in _choice
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py", line 137 in __enter__
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 276 in _model_spec_start_
File "/Applications/ChimeraX-1.7.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 245 in _model_range_
File "/Applications/ChimeraX-1.7.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 228 in _model_range_list_
File "/Applications/ChimeraX-1.7.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 213 in _model_hierarchy_
File "/Applications/ChimeraX-1.7.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/_atomspec.py", line 177 in _model_
File "/Applications/ChimeraX-1.7.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py", line 81 in parse
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 901 in parse
File "/Applications/ChimeraX-1.7.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.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.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.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.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.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.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.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, chimerax.mmcif.mmcif_write (total: 53)
{"app_name":"ChimeraX","timestamp":"2024-01-18 15:48:56.00 -0800","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.0 (23A344)","roots_installed":0,"name":"ChimeraX","incident_id":"BE760651-F0AE-4BB4-BACA-B9376E080D5A"}
{
"uptime" : 13000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,2",
"coalitionID" : 1859,
"osVersion" : {
"train" : "macOS 14.0",
"build" : "23A344",
"releaseType" : "User"
},
"captureTime" : "2024-01-18 15:48:53.0085 -0800",
"codeSigningMonitor" : 1,
"incident" : "BE760651-F0AE-4BB4-BACA-B9376E080D5A",
"pid" : 4241,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-01-18 15:16:43.4239 -0800",
"procStartAbsTime" : 266495269194,
"procExitAbsTime" : 312804124442,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"DC33E73C-FA52-5625-BB1C-E16B2534C308","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "D90B7D68-427E-98ED-CD16-515C91CC8B65",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 5347,
"sleepWakeUUID" : "C76EFC1E-A370-4B4F-8CFD-2EA3ABD300C9",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140722823462743\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc95e78000-7ffcbb598000 [599.1M] r-x\/r-x SM=COW ...t_id=b581fab3",
"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":4241},
"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: 140722823462743\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n mapped file 7ffc95e78000-7ffcbb598000 [599.1M] r-x\/r-x SM=COW ...t_id=b581fab3",
"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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]
}
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA
> W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc" format mrc
Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #1, grid size
448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32
> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif
---
warning | No mmCIF models found.
> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif
---
warning | No mmCIF models found.
> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1.cif
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1.cif
---
warnings | Unknown polymer entity '1' near line 61
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for FtsH_fresh_group1.cif #2
---
Chain | Description
A | No description available
> select add #2
3176 atoms, 3218 bonds, 406 residues, 1 model selected
> close #2
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
> final/ATP_C1_class1/FtsH_ATP_class1_refined.pdb"
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
final/ATP_C1_class1/FtsH_ATP_class1_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.003 0.027 3218
Ignored bad PDB record found on line 24
ANGLE : 0.551 7.969 4354
18 messages similar to the above omitted
Chain information for FtsH_ATP_class1_refined.pdb #2
---
Chain | Description
A | No description available
> select add #2
3176 atoms, 3218 bonds, 406 residues, 1 model selected
> close #2
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
> final/ATP_C1_class1/helix_ATP_C1_refined.pdb"
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
final/ATP_C1_class1/helix_ATP_C1_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.007 0.097 96540
Ignored bad PDB record found on line 24
ANGLE : 0.891 19.396 130620
18 messages similar to the above omitted
Chain information for helix_ATP_C1_refined.pdb #2
---
Chain | Description
1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description
available
> view orient
> hide atoms
> show cartoons
> view orient
> turn x -90 1 models #1
> view orient
> turn x -90 1 models #2
> view orient
> move y 5 1 models #2
> move z -5 1 models #2
> move y 5 1 models #2
> fitmap #2 inMap #1
Fit molecule helix_ATP_C1_refined.pdb (#2) to map
cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) using 97320 atoms
average map value = 0.3579, steps = 92
shifted from previous position = 2.86
rotated from previous position = 0.103 degrees
atoms outside contour = 82925, contour level = 0.89396
Position of helix_ATP_C1_refined.pdb (#2) relative to
cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999842 -0.00002522 0.00177879 -0.36620967
0.00002472 0.99999996 0.00028057 -4.70584854
-0.00177880 -0.00028053 0.99999838 -0.11217952
Axis -0.15577836 0.98769470 0.01386645
Axis point -27.81900309 0.00000000 608.03636134
Rotation angle (degrees) 0.10318725
Shift along axis -4.59244966
> view orient
> move y 2 1 models #2
> fitmap #2 inMap #1
Fit molecule helix_ATP_C1_refined.pdb (#2) to map
cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) using 97320 atoms
average map value = 0.3558, steps = 76
shifted from previous position = 2.04
rotated from previous position = 0.641 degrees
atoms outside contour = 82605, contour level = 0.89396
Position of helix_ATP_C1_refined.pdb (#2) relative to
cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99995635 0.00065020 -0.00932077 1.34280220
-0.00063582 0.99999860 0.00154569 -4.57588483
0.00932176 -0.00153970 0.99995537 0.04209690
Axis -0.16290479 -0.98430261 -0.06790001
Axis point -34.66049801 0.00000000 219.07481623
Rotation angle (degrees) 0.54259463
Shift along axis 4.28244807
> view orient
> move z -2 1 models #2
> view orient
> fitmap #2 inMap #1
Fit molecule helix_ATP_C1_refined.pdb (#2) to map
cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) using 97320 atoms
average map value = 1.775, steps = 76
shifted from previous position = 2.88
rotated from previous position = 0.559 degrees
atoms outside contour = 27882, contour level = 0.89396
Position of helix_ATP_C1_refined.pdb (#2) relative to
cryosparc_P3_J171_006_volume_map_sym_sharp.mrc (#1) coordinates:
Matrix rotation and translation
0.99999993 0.00026247 0.00028283 -0.14689119
-0.00026242 0.99999995 -0.00015807 0.10550173
-0.00028288 0.00015799 0.99999995 0.03686825
Axis 0.37900402 0.67836833 -0.62942224
Axis point 113.97586756 0.00000000 509.58952029
Rotation angle (degrees) 0.02389029
Shift along axis -0.00730901
> volume #1 step 1
> volume #1 level 1.5
> view orient
> hide #!1 models
> show #!1 models
> save /Users/yiyingli/untransoformed.cif relModel #2
Not saving entity_poly_seq for non-authoritative sequences
> save /Users/yiyingli/transformed.cif
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/yiyingli/transformed.cif
Summary of feedback from opening /Users/yiyingli/transformed.cif
---
warnings | Unknown polymer entity '1' near line 430
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for transformed.cif #3
---
Chain | Description
1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description
available
> open /Users/yiyingli/untransoformed.cif
Summary of feedback from opening /Users/yiyingli/untransoformed.cif
---
warnings | Unknown polymer entity '1' near line 430
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for untransoformed.cif #4
---
Chain | Description
1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description
available
> hide #!3 models
> hide #!4 models
> show #!4 models
> close #1
> open /Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif
> format mmcif
No such file/path: /Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/Deposition/FtsH_fresh_group1_BiologicalAssembly.cif
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/TO SAVE DATA
> W3/cryosparc_P3_J171_006_volume_map_sym_sharp.mrc" format mrc
Opened cryosparc_P3_J171_006_volume_map_sym_sharp.mrc as #1, grid size
448,448,448, pixel 0.86, shown at level 0.894, step 2, values float32
> hide #!2 models
> hide atoms
> show cartoons
> close #2
> open "/Users/yiyingli/Library/CloudStorage/OneDrive-
> UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
> final/ATP_C1_class1/helix_ATP_C1_refined.pdb" format pdb
Summary of feedback from opening
/Users/yiyingli/Library/CloudStorage/OneDrive-
UCSanDiego/FtsH_1D/CryoEM_1D/CryoEM
final/ATP_C1_class1/helix_ATP_C1_refined.pdb
---
warnings | Ignored bad PDB record found on line 20
Ignored bad PDB record found on line 21
GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
Ignored bad PDB record found on line 22
DEVIATIONS FROM IDEAL VALUES.
Ignored bad PDB record found on line 23
BOND : 0.007 0.097 96540
Ignored bad PDB record found on line 24
ANGLE : 0.891 19.396 130620
18 messages similar to the above omitted
Chain information for helix_ATP_C1_refined.pdb #2
---
Chain | Description
1 3 5 7 A C E G I K M O Q S U W Y a c e g i k m o q s u w y | No description
available
> hide atoms
> show cartoons
> hide #!4 models
> hide #!1 models
> show #!1 models
> volume #1 step 1
> volume #1 level 2
> view orient
> ui tool show "Side View"
> view
> set bgColor white
> hide #!1 models
> close #3
> show #!1 models
> close #4
> name extra #2/A,C,E,G,I
> select extra
15880 atoms, 16090 bonds, 2030 residues, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> name extra #2/A,C,E,G,I,w,1,3
> select extra
25408 atoms, 25744 bonds, 3248 residues, 1 model selected
> hide #!1 models
> name extra #2/A,C,E,G,I,w,1,3,5,7,y
> select extra
34936 atoms, 35398 bonds, 4466 residues, 1 model selected
> show #!1 models
> view orient
> select ~sel & ##selected
62384 atoms, 61142 bonds, 9754 residues, 1 model selected
> combine sel modelId 3
> hide #!2 models
> hide #!1 models
> show #!1 models
> select #3/A,C,E,G,I,w,1,3,5,7,y
34936 atoms, 35398 bonds, 4466 residues, 1 model selected
> delete sel
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> view orient
> save /Users/yiyingli/fresh_group1_assembly.cif models #3 relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/yiyingli/fresh_group1_assembly.cif
Summary of feedback from opening /Users/yiyingli/fresh_group1_assembly.cif
---
warnings | Unknown polymer entity '1' near line 342
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for fresh_group1_assembly.cif #4
---
Chain | Description
K M O Q S U W Y a c e g i k m o q s u | No description available
> hide atoms
> show cartoons
> hide #!3 models
> volume #1 level 1
> volume #1 level 2
> view orient
> close #3
> close #2
> renumber #4/W start 1 relative true
406 residues renumbered
> hide #!1 models
> hide #4.1 models
> undo
> ui tool show "Show Sequence Viewer"
> sequence chain /K /M /O /Q /S /U /W /Y /a /c /e /g /i /k /m /o /q /s /u
Alignment identifier is 1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 86
OpenGL renderer: Apple M2
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: Mac
Model Identifier: Mac14,2
Model Number: FLY13LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 8 GB
System Firmware Version: 10151.1.1
OS Loader Version: 10151.1.1
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 20 hours, 30 minutes
Graphics/Displays:
Apple M2:
Chipset Model: Apple M2
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina Display
Resolution: 2560 x 1664 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL U2414H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 50.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.13
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: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
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
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
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: 1.5.13
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: 1.0.3
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: 1.12.3
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: 1.33.2
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: 0.2.0
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: 4.47.0
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: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
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: 10.0.1
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
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: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 21 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 while parsing atom spec |
comment:2 by , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
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It looks like at some point we are going to have to buckle down and see if we can figure anything out about these crashes.