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Opened 19 months ago
Closed 19 months ago
#14806 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-14.0-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
Current thread 0x00007ff85dcf4e80 (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/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.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
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
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 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
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 2908 in run
File "/Applications/ChimeraX-1.7.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.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 375 in thread_safe
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
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.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite (total: 60)
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{
"uptime" : 1300000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookAir9,1",
"coalitionID" : 513,
"osVersion" : {
"train" : "macOS 14.0",
"build" : "23A344",
"releaseType" : "User"
},
"captureTime" : "2024-03-22 16:37:07.0076 +0000",
"codeSigningMonitor" : 0,
"incident" : "363070C4-9EC2-4E60-8E60-96919F2D769F",
"pid" : 41589,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-03-22 13:29:47.6212 +0000",
"procStartAbsTime" : 1312147173208309,
"procExitAbsTime" : 1318214905850911,
"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":"47B9A556-6B82-5ED9-8A87-7AA9017F29EB","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "E0226327-6B20-A20B-5B9D-FFB5A18EB828",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 86,
"bridgeVersion" : {"build":"21P365","train":"8.0"},
"sleepWakeUUID" : "0C4B25E9-F6E2-43E9-AC1A-E3E652061027",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487458135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff25000-7ffffff26000 [ 4K] r-x\/r-x SM=SHM ",
"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":41589},
"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: 140737487458135\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff25000-7ffffff26000 [ 4K] r-x\/r-x SM=SHM ",
"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 =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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/laotangmu233/Desktop/labelled RABV-G stracture at normal
> pH.pdb" format pdb
labelled RABV-G stracture at normal pH.pdb title:
Structure of rabies virus glycoprotein At basic pH [more info...]
Chain information for labelled RABV-G stracture at normal pH.pdb #1
---
Chain | Description | UniProt
A B | glycoprotein,glycoprotein,glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB
80-120, D8VEC1_9RHAB 126-439
> close
> open 6LGW format mmcif fromDatabase pdb
6lgw title:
Structure of Rabies virus glycoprotein in complex with neutralizing antibody
523-11 at acidic pH [more info...]
Chain information for 6lgw #1
---
Chain | Description | UniProt
A C | scFv 523-11 |
E F | Glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB 80-120, D8VEC1_9RHAB
126-405
6lgw mmCIF Assemblies
---
1| author_and_software_defined_assembly
2| author_and_software_defined_assembly
> select /A:1-224
1720 atoms, 1763 bonds, 1 pseudobond, 222 residues, 2 models selected
> hide sel cartoons
> select /C:1-224
1727 atoms, 1770 bonds, 1 pseudobond, 223 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select /F:1-397
2993 atoms, 3072 bonds, 2 pseudobonds, 378 residues, 2 models selected
> select /E:1-395
2902 atoms, 2977 bonds, 3 pseudobonds, 368 residues, 2 models selected
> hide sel cartoons
Drag select of 173 residues
> color sel green
> select /F:265
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
255 atoms, 256 bonds, 31 residues, 1 model selected
> color sel green
> select clear
> select /F:241
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
26 atoms, 27 bonds, 3 residues, 1 model selected
> select up
2993 atoms, 3072 bonds, 378 residues, 1 model selected
> select down
26 atoms, 27 bonds, 3 residues, 1 model selected
> select clear
Drag select of 61 residues
> select up
922 atoms, 935 bonds, 116 residues, 1 model selected
> select down
480 atoms, 61 residues, 1 model selected
> color sel blue
> select clear
> select /F:41
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
77 atoms, 78 bonds, 9 residues, 1 model selected
> color sel blue
> select clear
> select /F:203
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
48 atoms, 47 bonds, 7 residues, 1 model selected
> color sel blue
> select /F:209
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
22 atoms, 22 bonds, 3 residues, 1 model selected
> select up
2993 atoms, 3072 bonds, 378 residues, 1 model selected
> select down
22 atoms, 22 bonds, 3 residues, 1 model selected
> color sel blue
> select /F:218
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel blue
> select /F:220
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
26 atoms, 25 bonds, 4 residues, 1 model selected
> color sel blue
> select /F:196
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
72 atoms, 72 bonds, 9 residues, 1 model selected
> color sel blue
> select /F:211
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
40 atoms, 39 bonds, 5 residues, 1 model selected
> color sel blue
> select /F:217
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
27 atoms, 27 bonds, 3 residues, 1 model selected
> color sel blue
> select /F:37
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue
> select /F:254
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue
> select /F:229
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
10 atoms, 9 bonds, 2 residues, 1 model selected
> color sel blue
> select clear
Drag select of 113 residues, 1 pseudobonds
> color sel red
> select clear
> select /F:144
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
36 atoms, 37 bonds, 4 residues, 1 model selected
> color sel red
> select clear
> movie record
> turn y 2 180
> wait 180
> enocde
Unknown command: movie enocde
> movie record
Already recording a movie
> movie encode
Movie saved to /Users/laotangmu233/Desktop/movie.mp4
> open 6LGX
Summary of feedback from opening 6LGX fetched from pdb
---
note | Fetching compressed mmCIF 6lgx from
http://files.rcsb.org/download/6lgx.cif
6lgx title:
Structure of Rabies virus glycoprotein at basic pH [more info...]
Chain information for 6lgx #2
---
Chain | Description | UniProt
A B | Glycoprotein,Glycoprotein,Glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB
80-120, D8VEC1_9RHAB 126-439
6lgx mmCIF Assemblies
---
1| author_and_software_defined_assembly
> hide #!1 models
> show #!1 models
> hide #!1 models
> select #2/B:2-408
2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected
> select #2/A:1-419
2968 atoms, 3048 bonds, 3 pseudobonds, 377 residues, 2 models selected
> hide sel cartoons
> show #!1 models
> hide #!1 models
> select #2/A:1-419
2968 atoms, 3048 bonds, 3 pseudobonds, 377 residues, 2 models selected
> select #2/B:2-408
2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected
> select clear
> select #2/B:395
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
144 atoms, 148 bonds, 19 residues, 1 model selected
> select up
2727 atoms, 2802 bonds, 348 residues, 1 model selected
> select down
144 atoms, 148 bonds, 19 residues, 1 model selected
> select clear
Drag select of 113 residues
> select clear
Drag select of 21 residues
> color green
> select clear
Drag select of 46 residues
> select clear
Drag select of 49 residues
> color blue
> undo
> show #!1 models
> hide #!1 models
> select clear
Drag select of 157 residues, 1 pseudobonds
> color sel green
> select #2/B:294
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
127 atoms, 126 bonds, 16 residues, 1 model selected
> color sel green
> select #2/B:320
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 2 residues, 1 model selected
> color sel green
> select clear
> select #2/B:12
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel green
> select clear
Drag select of 72 residues
> select up
692 atoms, 703 bonds, 90 residues, 1 model selected
> select down
557 atoms, 72 residues, 1 model selected
> color sel blue
> select #2/B:32
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
122 atoms, 122 bonds, 17 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> select #2/B:33
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel blue
> select #2/B:228
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> select #2/B:253
7 atoms, 7 bonds, 1 residue, 1 model selected
> select up
126 atoms, 128 bonds, 16 residues, 1 model selected
> select down
7 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
Drag select of 13 residues
> color sel blue
> select #2/B:215
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel blue
Drag select of 86 residues, 2 pseudobonds
> color sel red
> select #2/B:153
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
185 atoms, 189 bonds, 25 residues, 1 model selected
> color sel red
> select #2/B:146
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
50 atoms, 51 bonds, 6 residues, 1 model selected
> color sel red
> select #2/B:187
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
89 atoms, 91 bonds, 11 residues, 1 model selected
> color sel red
> select #2/B:54
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> show #!1 models
> matchmaker 6lgw to 6lgx
Missing or invalid "matchAtoms" argument: invalid atoms specifier
> matchmaker #6lgw to #6lgx
Missing or invalid "matchAtoms" argument: only initial part "#6" of atom
specifier valid
> 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 6lgx, chain A (#2) with 6lgw, chain F (#1), sequence alignment
score = 1971.4
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)
> matchmaker #1:262-390 to #2:262-390
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 6lgx, chain A (#2) with 6lgw, chain F (#1), sequence alignment
score = 598.6
RMSD between 96 pruned atom pairs is 0.747 angstroms; (across all 121 pairs:
3.732)
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> mmaker #1:1-190 to #2:1-190
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 6lgx, chain A (#2) with 6lgw, chain F (#1), sequence alignment
score = 818.5
RMSD between 94 pruned atom pairs is 0.649 angstroms; (across all 162 pairs:
26.177)
> save "/Users/laotangmu233/Desktop/matchermarker two proteins.cxs"
> ui tool show Matchmaker
> select ~sel & ##selected
Nothing selected
> mmaker #1/B:1-190 to #2/F:1-190
No 'to' model specified
> mmaker #1/B to #2/F
No 'to' model specified
> mmaker #2/F to #1/B
No 'to' model specified
> mmaker #2/F #1/B
> matchmaker #2/F #1/B
Missing required "to" argument
> mmaker #2/F to #1/B
No 'to' model specified
> ui tool show Matchmaker
> matchmaker #!2 to #1/E pairing bs
Parameters
---
Chain pairing | bs
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 6lgw, chain E (#1) with 6lgx, chain A (#2), sequence alignment
score = 1895.2
RMSD between 31 pruned atom pairs is 0.647 angstroms; (across all 350 pairs:
41.759)
> hide #!1 models
> select #2
5695 atoms, 5850 bonds, 6 pseudobonds, 725 residues, 2 models selected
> show cartoons
> select #1
9342 atoms, 9582 bonds, 7 pseudobonds, 1191 residues, 2 models selected
> show sel cartoons
> show #!1 models
> hide #!2 models
> open 6lgx
6lgx title:
Structure of Rabies virus glycoprotein at basic pH [more info...]
Chain information for 6lgx #3
---
Chain | Description | UniProt
A B | Glycoprotein,Glycoprotein,Glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB
80-120, D8VEC1_9RHAB 126-439
6lgx 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 6lgw, chain F (#1) with 6lgx, chain A (#3), sequence alignment
score = 1971.4
RMSD between 23 pruned atom pairs is 1.228 angstroms; (across all 355 pairs:
33.765)
> hide #!1 models
> show #!1 models
> select #3/B
2727 atoms, 2802 bonds, 3 pseudobonds, 348 residues, 2 models selected
> hide sel cartoons
> hide #!3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/E #1/F
Alignment identifier is 1
> select
> #1/E-F:5-11,15-16,37-46,55-69,81-87,127-143,148-150,158-159,169-170,176-180,192-201,206-210,216-218,223-227,230-234,240-242,310-318,321-332,346-347,350-351,364-365,371-372
2058 atoms, 2064 bonds, 260 residues, 1 model selected
> show #!3 models
> open /Users/laotangmu233/Desktop/test.rtf
Unrecognized file suffix '.rtf'
> open /Users/laotangmu233/Desktop/test.cxc
> {\rtf1\ansi\ansicpg1252\cocoartf2757
Unknown command: {\rtf1\ansi\ansicpg1252\cocoartf2757
> open /Users/laotangmu233/Desktop/test.cxc
> {\rtf1\ansi\ansicpg1252\cocoartf2757
Failed opening file /Users/laotangmu233/Desktop/test.cxc:
Unknown command: {\rtf1\ansi\ansicpg1252\cocoartf2757
> open /Users/laotangmu233/Downloads/6lgx.pdb
6lgx.pdb title:
Structure of rabies virus glycoprotein At basic pH [more info...]
Chain information for 6lgx.pdb #4
---
Chain | Description | UniProt
A B | glycoprotein,glycoprotein,glycoprotein | Q5JZZ2_9RHAB 1-74, Q2Z2I1_9RHAB
80-120, D8VEC1_9RHAB 126-439
> open /Users/laotangmu233/Desktop/chimera_script.cxc
> Open 6lgw
Unknown command: Open 6lgw
> save /Users/laotangmu233/Desktop/MM.cxs
> close
> open /Users/laotangmu233/Desktop/MM.cxs format session
===== 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 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.1.27
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel 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 Air
Model Identifier: MacBookAir9,1
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.1 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)
OS Loader Version: 580~439
Software:
System Software Overview:
System Version: macOS 14.0 (23A344)
Kernel Version: Darwin 23.0.0
Time since boot: 56 days, 2 hours, 30 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a51
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 19 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 , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Yuhao,
--Eric