![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 18 months ago
Closed 18 months ago
#15089 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-13.5.1-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 0x0000700014efe000 (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 0x00007ff844f9d700 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 463 in new_pseudobond
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/clashes/cmd.py", line 230 in _cmd
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/clashes/cmd.py", line 54 in cmd_contacts
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/clashes/tool.py", line 59 in run_command
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, lxml._elementpath, lxml.etree, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast (total: 64)
{"app_name":"ChimeraX","timestamp":"2024-05-02 23:16:39.00 +0800","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 13.5.1 (22G90)","roots_installed":0,"name":"ChimeraX","incident_id":"5D9E9180-F4CE-49F1-B406-B4C8847C0107"}
{
"uptime" : 440000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 617,
"osVersion" : {
"train" : "macOS 13.5.1",
"build" : "22G90",
"releaseType" : "User"
},
"captureTime" : "2024-05-02 23:16:33.1523 +0800",
"incident" : "5D9E9180-F4CE-49F1-B406-B4C8847C0107",
"pid" : 60691,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-04-24 11:30:33.5874 +0800",
"procStartAbsTime" : 132386735379063,
"procExitAbsTime" : 449225505783257,
"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":"A6D81A79-8089-5BB5-A608-2D8026D97791","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "5D94D93A-2DE6-BE74-A8FC-FB8F22FB1355",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 12839,
"bridgeVersion" : {"build":"20P6072","train":"7.6"},
"sleepWakeUUID" : "DABFED0A-37A5-452F-AB09-D40134A6A572",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487339351\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff08000-7ffffff09000 [ 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":60691},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487339351\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff08000-7ffffff09000 [ 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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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
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"size" : 49152,
"uuid" : "3a3fa85c-f1fe-336c-bf68-924fc947ade3",
"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
"name" : "libsystem_pthread.dylib"
},
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"size" : 557048,
"uuid" : "d5b303ad-54f4-323b-bbe2-2d0f34c45649",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
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"size" : 40944,
"uuid" : "f1798256-c6b5-335c-bbb5-7978acf41deb",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
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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
> /Users/kelvinchung/Downloads/BPHM4142_Lab1_hLcn2_758d7/BPHM4142_Lab1_hLcn2_758d7_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
> format pdb
Chain information for
BPHM4142_Lab1_hLcn2_758d7_unrelaxed_rank_004_alphafold2_ptm_model_1_seed_000.pdb
#1
---
Chain | Description
A | No description available
> hide target m
> show #1 models
> close
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/Heavy_Light_chains_rank_1.pdb"
Chain information for Heavy_Light_chains_rank_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 2 document/hLcn2.pdb"
Chain information for hLcn2.pdb #2
---
Chain | Description
A | No description available
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 2 document/C87A.pdb"
Chain information for C87A.pdb #3
---
Chain | Description
A | No description available
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 2 document/R81E.pdb"
Chain information for R81E.pdb #4
---
Chain | Description
A | No description available
> hide #2 models
> hide #3 models
> hide #4 models
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> save "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/BPHM4142_Lab 3_Proteins.cxs"
> set bgColor white
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/heavy_rank_1.pdb"
Chain information for heavy_rank_1.pdb #5
---
Chain | Description
A | No description available
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/light_rank_1.pdb"
Chain information for light_rank_1.pdb #6
---
Chain | Description
A | No description available
> ui tool show "Show Sequence Viewer"
> select clear
> ui tool show Matchmaker
> matchmaker #5-6 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 Heavy_Light_chains_rank_1.pdb, chain A (#1) with heavy_rank_1.pdb,
chain A (#5), sequence alignment score = 594.4
RMSD between 117 pruned atom pairs is 0.555 angstroms; (across all 123 pairs:
1.086)
Matchmaker Heavy_Light_chains_rank_1.pdb, chain B (#1) with light_rank_1.pdb,
chain A (#6), sequence alignment score = 536.7
RMSD between 107 pruned atom pairs is 0.233 angstroms; (across all 107 pairs:
0.233)
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #5/A
Alignment identifier is 1
> sequence chain #1/B #6/A
Alignment identifier is 2
> hide #5 models
> show #5 models
> hide #5 models
> hide #6 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> surface #1
> surface hidePatches #1
> select #1/A:13-14 #5/A:13-14
32 atoms, 32 bonds, 4 residues, 2 models selected
> select #1/A:13-17 #5/A:13-17
60 atoms, 60 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [13-17] RMSD: 0.169
> select #1/A:26-27 #5/A:26-27
26 atoms, 26 bonds, 4 residues, 2 models selected
> select #1/A:26-31 #5/A:26-31
74 atoms, 74 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [26-31] RMSD: 3.242
> surface (#!1 & sel)
> undo
> select clear
> surface #1
> cartoon hide #1
> select clear
> surface hidePatches #1
> cartoon #1
> hide #!1 models
> show #2 models
> surface #2
> surface hidePatches #2
> sel: 81, 87
Unknown command: sel: 81, 87
> sel: 81
Unknown command: sel: 81
> sel:81, 87
Unknown command: sel:81, 87
> sel:81
Unknown command: sel:81
> sel: 81
Unknown command: sel: 81
> select: 81
Unknown command: select: 81
> select: 81
Unknown command: select: 81
> sel: /81
Unknown command: sel: /81
> select :81
61 atoms, 54 bonds, 7 residues, 6 models selected
> select clear
> select :81,87
118 atoms, 106 bonds, 14 residues, 6 models selected
> select clear
> surface #2
> select :81,87
118 atoms, 106 bonds, 14 residues, 6 models selected
> hide #!2 models
> show #!1 models
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #3 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> select clear
> select :1
61 atoms, 54 bonds, 7 residues, 6 models selected
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> select #3/A:81-82
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:81-90
72 atoms, 74 bonds, 10 residues, 1 model selected
> color sel red
> color sel orange
> color sel forest green
> color sel blue
> color sel orange red
> select clear
> select #3/A:92
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #3/A:92-101
80 atoms, 82 bonds, 10 residues, 1 model selected
> color sel forest green
> color sel orange
> undo
> color sel forest green
> select clear
> surface #3
> surface hidePatches #3
> select #3/A:92-93
18 atoms, 18 bonds, 2 residues, 1 model selected
> select #3/A:92-101
80 atoms, 82 bonds, 10 residues, 1 model selected
> surface (#!3 & sel)
> select #3/A:81
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #3/A:81-89
68 atoms, 70 bonds, 9 residues, 1 model selected
> select #3/A:81-82
18 atoms, 17 bonds, 2 residues, 1 model selected
> select #3/A:81-90
72 atoms, 74 bonds, 10 residues, 1 model selected
> surface (#!3 & sel)
> select clear
> select :81-90, 92-101
1098 atoms, 1122 bonds, 140 residues, 6 models selected
> surface (#!3 & sel)
> surface hidePatches (#!3 & sel)
> select :81-90, 92-101
1098 atoms, 1122 bonds, 140 residues, 6 models selected
> select add #2
2396 atoms, 2453 bonds, 298 residues, 10 models selected
> select subtract #2
945 atoms, 965 bonds, 120 residues, 9 models selected
> select add #1
2345 atoms, 2397 bonds, 310 residues, 8 models selected
> select subtract #1
624 atoms, 638 bonds, 80 residues, 7 models selected
> select add #4
1922 atoms, 1969 bonds, 238 residues, 5 models selected
> select subtract #4
473 atoms, 483 bonds, 60 residues, 4 models selected
> select add #5
1226 atoms, 1255 bonds, 163 residues, 4 models selected
> select subtract #5
308 atoms, 317 bonds, 40 residues, 3 models selected
> select add #6
955 atoms, 977 bonds, 127 residues, 3 models selected
> select subtract #6
152 atoms, 156 bonds, 20 residues, 2 models selected
> select add #3
1450 atoms, 1487 bonds, 178 residues, 2 models selected
> select subtract #3
1 model selected
> select add #3
1450 atoms, 1487 bonds, 178 residues, 1 model selected
> select subtract #3
1 model selected
> select :81-90, 92-101
1098 atoms, 1122 bonds, 140 residues, 6 models selected
> surface (#!3 & sel)
> select :81-90
558 atoms, 568 bonds, 70 residues, 6 models selected
> select clear
> surface hidePatches #3
> select :81-90
558 atoms, 568 bonds, 70 residues, 6 models selected
> surface (#!3 & sel)
> color (#!3 & sel) orange red
> select clear
> select :92-101
540 atoms, 554 bonds, 70 residues, 6 models selected
> surface (#!3 & sel)
> select clear
> surface hidePatches #3
> surface #3
> select :92-101
540 atoms, 554 bonds, 70 residues, 6 models selected
> color (#!3 & sel) forest green
> hide #!3 models
> show #4 models
> select :1
61 atoms, 54 bonds, 7 residues, 6 models selected
> select clear
> select :71-90
1165 atoms, 1193 bonds, 140 residues, 6 models selected
> color (#4 & sel) orange red
> select clear
> select : 95-105
567 atoms, 576 bonds, 77 residues, 6 models selected
> color (#4 & sel) forest green
> color (#4 & sel) blue
> select clear
> surface #4
> surface hidePatches #4
> surface #4
> select : 95-105
567 atoms, 576 bonds, 77 residues, 6 models selected
> color (#!4 & sel) blue
> select clear
> select : 71-90
1165 atoms, 1193 bonds, 140 residues, 6 models selected
> color (#!4 & sel) orange
> color (#!4 & sel) orange red
> hide #!4 models
> show #!1 models
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A #5/A
Alignment identifier is 1
> sequence chain #1/B #6/A
Alignment identifier is 2
> select #1/A:122-123 #5/A:122-123
24 atoms, 22 bonds, 4 residues, 2 models selected
> select #1/A:122-123 #5/A:122-123
24 atoms, 22 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [122-123] RMSD: 2.951
> select clear
> select #5/A
918 atoms, 938 bonds, 123 residues, 1 model selected
> select clear
> select #1/A
918 atoms, 938 bonds, 123 residues, 1 model selected
> color (#!1 & sel) orange
> select clear
> select #1/B
803 atoms, 821 bonds, 107 residues, 1 model selected
> color (#!1 & sel) cyan
> select clear
> select strand
3505 atoms, 3540 bonds, 424 residues, 6 models selected
> color (#!1 & sel) magenta
> select clear
> select #1/A:104 #5/A:104
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:104-116 #5/A:104-116
216 atoms, 228 bonds, 26 residues, 2 models selected
1 [ID: 1] region 2 chains [104-116] RMSD: 1.927
> select clear
> surface #1
> surface hidePatches #1
> select #1/A:1 #5/A:1
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #1/A:1-2 #5/A:1-2
32 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [1-2] RMSD: 0.996
> select clear
> select #1/A:122 #5/A:122
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/A:122-123 #5/A:122-123
24 atoms, 22 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [122-123] RMSD: 2.951
> select clear
> hide #!1 models
> show #5 models
> show #6 models
> surface #5-6
> surface hidePatches #5-6
> surface #5-6
> hide #!5 models
> hide #!6 models
> show #!1 models
> hide #!1 models
> show #!5 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> show #!1 models
> select #1/A:122 #5/A:122
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/A:122-123 #5/A:122-123
24 atoms, 22 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [122-123] RMSD: 2.951
> select clear
> surface #1
> surface hidePatches #1
> surface #1
> surface hidePatches #1
> surface #1
> surface hidePatches #1
> surface #1
> surface hidePatches #1
> select #1/A:28 #5/A:28
12 atoms, 10 bonds, 2 residues, 2 models selected
> select #1/A:28-35 #5/A:28-35
114 atoms, 114 bonds, 16 residues, 2 models selected
1 [ID: 1] region 2 chains [28-35] RMSD: 2.803
> color (#!1 & sel) red
> select #1/A:55-56 #5/A:55-56
20 atoms, 18 bonds, 4 residues, 2 models selected
> select #1/A:55-60 #5/A:55-60
60 atoms, 58 bonds, 12 residues, 2 models selected
1 [ID: 1] region 2 chains [55-60] RMSD: 0.266
> color (#!1 & sel) red
> select clear
> select strand
3505 atoms, 3540 bonds, 424 residues, 6 models selected
> select clear
> select strand
3505 atoms, 3540 bonds, 424 residues, 6 models selected
> color (#!1 & sel) light gray
> color (#!1 & sel) lime
> color (#!1 & sel) cornflower blue
> color (#!1 & sel) lime
> color (#!1 & sel) medium blue
> color (#!1 & sel) forest green
> select clear
> select #1/A:104 #5/A:104
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #1/A:104-108 #5/A:104-108
72 atoms, 76 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [104-108] RMSD: 2.746
> color (#!1 & sel) red
> select #1/B:26-27 #6/A:26-27
30 atoms, 28 bonds, 4 residues, 2 models selected
> select #1/B:26-32 #6/A:26-32
106 atoms, 106 bonds, 14 residues, 2 models selected
2 [ID: 2] region chains A,B [26-32] RMSD: 0.172
> color (#!1 & sel) red
> select #1/B:99 #6/A:99
8 atoms, 6 bonds, 2 residues, 2 models selected
> select #1/B:91-99 #6/A:91-99
126 atoms, 130 bonds, 18 residues, 2 models selected
2 [ID: 2] region chains A,B [91-99] RMSD: 0.390
> color (#!1 & sel) red
> select #1/B:49 #6/A:49
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #1/B:49-61 #6/A:49-61
184 atoms, 186 bonds, 26 residues, 2 models selected
2 [ID: 2] region chains A,B [49-61] RMSD: 0.261
> color (#!1 & sel) red
> select strand
3505 atoms, 3540 bonds, 424 residues, 6 models selected
> select clear
> hide #!1 models
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/BPHM4142 Lab 3 Report.docx"
Unrecognized file suffix '.docx'
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/Antibody_hLcn2_rank_1.pdb"
Chain information for Antibody_hLcn2_rank_1.pdb #7
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show Contacts
> help help:user/tools/clashes.html
> alphafold contacts /A toResidues /B distance 5
Interface PAE pseudobonds can only be computed for a single structure, got 7.
> ui tool show Contacts
> hide #!1 target m
> hide #!2 target m
> hide #!3 target m
> hide #!4 target m
> hide #!5 target m
> hide #!6 target m
> show #7 target m
> alphafold contacts /A toResidues /B distance 5
Interface PAE pseudobonds can only be computed for a single structure, got 7.
> hide #7 models
> show #!1 models
> save "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/BPHM4142 Lab 3 Antibody CDR prediction.pdb" models
> #1 relModel #1
> show #!2 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> close #1
> close #2
> close #3
> close #4
> close #5
> close #6
> show #7 models
> alphafold contacts /A toResidues /B distance 5
Structure Antibody_hLcn2_rank_1.pdb #7 does not have PAE data opened
> ui tool show Contacts
> ui tool show "Selection Inspector"
> ui tool show "AlphaFold Error Plot"
> help help:user/tools/alphafold.html#pae
Must choose path to predicted aligned file
> ui tool show "AlphaFold Error Plot"
> help help:user/tools/alphafold.html#pae
> surface
> surface hidePatches
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #7 does not have PAE data opened
> ui tool show Contacts
> ui tool show AlphaFold
Must choose path to predicted aligned file
> close #7
> open "/Users/kelvinchung/Desktop/BPHM Year 4 Sem 2 Files/BPHM4142 Mol. Pharm
> Document/Lab 3 document/Antibody_hLcn2_rank_1.pdb"
Chain information for Antibody_hLcn2_rank_1.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> ui tool show "AlphaFold Error Plot"
> alphafold pae #1 uniprotId
Missing "uniprotId" keyword's argument
> ui tool show Contacts
> help help:user/tools/clashes.html
> contacts sel distanceOnly 4.9999999999999964 intraModel false intraMol false
> ignoreHiddenModels true showDist true reveal true
No atoms match given atom specifier
> ui tool show Contacts
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> alphafold contacts /A toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> select /A
918 atoms, 938 bonds, 123 residues, 1 model selected
> select /B
803 atoms, 821 bonds, 107 residues, 1 model selected
> alphafold contacts /C toResidues /B
Structure Antibody_hLcn2_rank_1.pdb #1 does not have PAE data opened
> select clear
> ui tool show "AlphaFold Error Plot"
File "iojoih" does not exist.
> help help:user/tools/alphafold.html#pae
> select clear
> select /C
1451 atoms, 1488 bonds, 178 residues, 1 model selected
> hide sel cartoons
> show sel atoms
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> sequence chain /B
Alignment identifier is 1/B
> select clear
> select /C
1451 atoms, 1488 bonds, 178 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select /A:122
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:122-123
12 atoms, 11 bonds, 2 residues, 1 model selected
> select clear
> select /C
1451 atoms, 1488 bonds, 178 residues, 1 model selected
> show sel cartoons
> hide sel cartoons
> select clear
> select /A:122-123
12 atoms, 11 bonds, 2 residues, 1 model selected
> select /A:122-123
12 atoms, 11 bonds, 2 residues, 1 model selected
> select clear
> select /C
1451 atoms, 1488 bonds, 178 residues, 1 model selected
> show sel cartoons
> select clear
> ui tool show Contacts
> contacts sel distanceOnly 5.0 interModel false ignoreHiddenModels true
> showDist true reveal true
No atoms match given atom specifier
> ui tool show Contacts
> contacts sel distanceOnly 5.0 intraRes true ignoreHiddenModels true showDist
> true reveal true
No atoms match given atom specifier
> ui tool show Contacts
> contacts sel intraRes true ignoreHiddenModels true showDist true reveal true
No atoms match given atom specifier
> ui tool show Contacts
> contacts sel intraRes true ignoreHiddenModels true showDist true reveal true
No atoms match given atom specifier
> select /C
1451 atoms, 1488 bonds, 178 residues, 1 model selected
> ui tool show Contacts
> contacts sel distanceOnly 5.0 intraRes true ignoreHiddenModels true showDist
> true reveal true
9784 distances
===== 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-4.14.1
OpenGL renderer: AMD Radeon Pro 5500M 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: 2.3 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: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.5.1 (22G90)
Kernel Version: Darwin 22.6.0
Time since boot: 12日5小時57分鐘
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 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
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: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 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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