![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17410 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.2-arm64-arm-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 0x000000035d05f000 (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 0x0000000204854f80 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/weakref.py", line 575 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1613 in remove_deleted_pointers
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 391 in __init__
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 2226 in process_changes
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 2231 in changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.mmcif.mmcif_write (total: 54)
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"procRole" : "Foreground",
"version" : 2,
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"releaseType" : "User"
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"captureTime" : "2025-04-17 10:26:13.7796 -0400",
"codeSigningMonitor" : 1,
"incident" : "CC7012FD-73D2-467D-9FEF-42A96F573379",
"pid" : 28552,
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"procLaunch" : "2025-04-16 22:02:38.5557 -0400",
"procStartAbsTime" : 4173059836546,
"procExitAbsTime" : 4369604208782,
"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"},
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1C35DA4E-79D7-2EAA-1474-0E84CDD7BB46",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
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"codeSigningTrustLevel" : 4294967295,
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"wakeTime" : 3887,
"sleepWakeUUID" : "52588AFB-F7E5-4C9F-AA09-A6BED8BE1883",
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 4333485911\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1024bc000-1024c0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":28552},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 4333485911\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1024bc000-1024c0000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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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/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final-
> files/M_PRO-120538_.pdb
Chain information for M_PRO-120538_.pdb #1
---
Chain | Description
H | No description available
L | No description available
M | No description available
> save /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/M_PRO-120538.cif relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final-
> files/M_PRO-120538.cif
Summary of feedback from opening
/Users/pfeliciano/Library/CloudStorage/OneDrive-
GenerateBiomedicines/Documents/Projects/Outer-
Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final-
files/M_PRO-120538.cif
---
warnings | Unknown polymer entity '1' near line 124
Unknown polymer entity '2' near line 1624
Unknown polymer entity '3' near line 3177
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for M_PRO-120538.cif #2
---
Chain | Description
H | No description available
L | No description available
M | No description available
> hide #!1 models
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120538/G-PDB-to-deposit/final-
> files/M_PRO-120538.mrc
Opened M_PRO-120538.mrc as #3, grid size 300,300,300, pixel 0.81, shown at
level 0.0735, step 2, values float32
> volume #3 step 1
> volume #3 level 0.22
> surface dust #3 size 8.1
> transparency 50
> close
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final-
> files/M_PRO-120549_.pdb
Chain information for M_PRO-120549_.pdb #1
---
Chain | Description
H | No description available
L | No description available
M | No description available
> save /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/M_PRO-120549.cif relModel #1
Not saving entity_poly_seq for non-authoritative sequences
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final-
> files/M_PRO-120549.cif
Summary of feedback from opening
/Users/pfeliciano/Library/CloudStorage/OneDrive-
GenerateBiomedicines/Documents/Projects/Outer-
Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final-
files/M_PRO-120549.cif
---
warnings | Unknown polymer entity '1' near line 124
Unknown polymer entity '2' near line 1683
Unknown polymer entity '3' near line 3209
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for M_PRO-120549.cif #2
---
Chain | Description
H | No description available
L | No description available
M | No description available
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120549/G-PDB-to-deposit/final-
> files/M_PRO-120549.mrc
Opened M_PRO-120549.mrc as #3, grid size 288,288,288, pixel 0.888, shown at
level 0.0764, step 2, values float32
> volume #3 step 1
> volume #3 level 0.3047
> surface dust #3 size 8.88
> transparency 50
> hide #!3 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> volume #3 level 0.1763
> close #1
> close
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120446/cryosparc-
> maps/cryosparc_P651_J24_006_volume_map.mrc
Opened cryosparc_P651_J24_006_volume_map.mrc as #1, grid size 240,240,240,
pixel 1.01, shown at level 0.0244, step 1, values float32
> volume #1 level 0.1073
> volume #1 level 0.1768
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120446/docking/M.pdb
Chain information for M.pdb #2
---
Chain | Description
M | No description available
> transparency 50
> ui mousemode right select
> select /M:453
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,14.681,0,1,0,27.996,0,0,1,27.878
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.86738,-0.33462,-0.36834,123.44,-0.019404,-0.76236,0.64687,169.61,-0.49726,-0.55393,-0.66775,384.29
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.86738,-0.33462,-0.36834,129.78,-0.019404,-0.76236,0.64687,139.8,-0.49726,-0.55393,-0.66775,379.39
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.71314,-0.18001,-0.67751,339.2,-0.25638,-0.83254,0.49107,198.06,-0.65245,0.5239,0.54757,94.201
> view matrix models
> #2,-0.98061,-0.028674,0.19385,233.29,0.15835,-0.69869,0.69768,103.63,0.11544,0.71485,0.68969,-40.717
> view matrix models
> #2,0.65813,0.66719,0.34888,-71.68,0.23386,-0.62161,0.7476,77.982,0.71566,-0.41043,-0.56513,203.17
> view matrix models
> #2,0.85394,0.042596,-0.51862,103.16,0.43109,-0.61613,0.65921,65.871,-0.29146,-0.78649,-0.5445,368.23
> view matrix models
> #2,0.97954,-0.07836,-0.18539,58.671,0.18431,-0.020785,0.98265,-25.4,-0.080853,-0.99671,-0.0059165,297.33
> view matrix models
> #2,0.91322,-0.15335,-0.37751,102.24,0.31436,-0.32432,0.89219,10.54,-0.25925,-0.93344,-0.24796,343.14
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.91322,-0.15335,-0.37751,111.53,0.31436,-0.32432,0.89219,46.276,-0.25925,-0.93344,-0.24796,370.37
> view matrix models
> #2,0.91322,-0.15335,-0.37751,119.27,0.31436,-0.32432,0.89219,37.968,-0.25925,-0.93344,-0.24796,349.02
> view matrix models
> #2,0.91322,-0.15335,-0.37751,88.281,0.31436,-0.32432,0.89219,2.2807,-0.25925,-0.93344,-0.24796,335.71
> view matrix models
> #2,0.91322,-0.15335,-0.37751,84.428,0.31436,-0.32432,0.89219,0.26385,-0.25925,-0.93344,-0.24796,328.92
> view matrix models
> #2,0.91322,-0.15335,-0.37751,82.348,0.31436,-0.32432,0.89219,-2.0106,-0.25925,-0.93344,-0.24796,327.22
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.63338,-0.77195,0.054041,286.92,0.64554,-0.48857,0.587,21.249,-0.42673,0.40668,0.80778,31.332
> view matrix models
> #2,-0.81837,0.25488,0.51508,114.09,0.3214,-0.54002,0.77787,40.437,0.47642,0.80213,0.36002,-65.999
> view matrix models
> #2,-0.70139,-0.29119,-0.65059,328.58,-0.053967,0.93182,-0.35888,49.465,0.71074,-0.21661,-0.66928,176.98
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.70139,-0.29119,-0.65059,335.3,-0.053967,0.93182,-0.35888,49.905,0.71074,-0.21661,-0.66928,170.74
> view matrix models
> #2,-0.70139,-0.29119,-0.65059,336.26,-0.053967,0.93182,-0.35888,49.008,0.71074,-0.21661,-0.66928,169.38
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.97251,0.21204,-0.096276,-2.198,-0.18938,0.47955,-0.85684,190.83,-0.13552,0.85151,0.50652,-27.252
> view matrix models
> #2,0.65446,0.7485,0.10691,-61.13,-0.31718,0.40014,-0.85982,216.62,-0.68636,0.5288,0.49928,80.615
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.65446,0.7485,0.10691,-67.21,-0.31718,0.40014,-0.85982,218.17,-0.68636,0.5288,0.49928,87.272
> view matrix models
> #2,0.65446,0.7485,0.10691,-67.795,-0.31718,0.40014,-0.85982,218.58,-0.68636,0.5288,0.49928,88.135
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.98875,0.031142,-0.14633,253.79,0.091881,0.8983,-0.42966,47.595,0.11807,-0.43827,-0.89105,305.8
> view matrix models
> #2,-0.73128,-0.28844,-0.61809,328.38,-0.034634,0.92072,-0.38869,54.156,0.6812,-0.26283,-0.68329,188.26
> view matrix models
> #2,-0.62632,0.073332,0.77611,80.327,0.29153,-0.9013,0.32043,154.04,0.723,0.42695,0.54312,-71.81
> view matrix models
> #2,0.98588,-0.093341,0.13902,-3.0098,-0.16728,-0.51228,0.84237,87.58,-0.0074124,-0.85373,-0.52066,323.98
> view matrix models
> #2,0.96203,-0.066266,-0.26479,51.074,0.21115,-0.43408,0.87578,28.104,-0.17298,-0.89843,-0.40361,333.5
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96203,-0.066266,-0.26479,54.178,0.21115,-0.43408,0.87578,29.177,-0.17298,-0.89843,-0.40361,330.9
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.95353,0.11359,0.27907,184.43,0.030514,-0.88505,0.4645,164.44,0.29975,0.45143,0.84045,-67.683
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.95353,0.11359,0.27907,187.6,0.030514,-0.88505,0.4645,165.96,0.29975,0.45143,0.84045,-70.5
> fitmap #2 inMap #1
Fit molecule M.pdb (#2) to map cryosparc_P651_J24_006_volume_map.mrc (#1)
using 2869 atoms
average map value = 0.2367, steps = 88
shifted from previous position = 1.96
rotated from previous position = 16.4 degrees
atoms outside contour = 1032, contour level = 0.1768
Position of M.pdb (#2) relative to cryosparc_P651_J24_006_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
-0.99487046 -0.01208539 0.10043247 232.52816565
0.04133776 -0.95472591 0.29460073 197.17801270
0.09232512 0.29724122 0.95032820 -41.09388798
Axis 0.04880821 0.14986057 0.98750168
Axis point 115.92943955 103.29969258 0.00000000
Rotation angle (degrees) 178.44998031
Shift along axis 0.31820898
> ui mousemode right select
> select clear
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-1-107.pdb
Summary of feedback from opening
/Users/pfeliciano/Library/CloudStorage/OneDrive-
GenerateBiomedicines/Documents/Projects/Outer-
Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-1-107.pdb
---
warnings | Ignored bad PDB record found on line 818
Ignored bad PDB record found on line 819
Chain information for PRO-120446-LC-1-107.pdb #3
---
Chain | Description
B | No description available
Drag select of 107 residues
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,120.07,0,1,0,195.59,0,0,1,91.346
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.14032,0.72388,-0.67551,133.59,0.22901,-0.64003,-0.73342,186.47,-0.96326,-0.25761,-0.075972,99.05
> view matrix models
> #3,0.32037,-0.90251,0.28781,100.62,-0.34471,-0.39407,-0.85199,188.46,0.88235,0.17374,-0.43735,119.52
> view matrix models
> #3,-0.73363,0.42935,-0.52673,124.51,0.30011,-0.49073,-0.818,190.03,-0.60969,-0.75819,0.23116,89.836
> ui mousemode right "translate selected models"
> ui mousemode right select
> select clear
> select #3/B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.27261,0.87117,-0.40835,130.84,-0.96188,-0.23726,0.13598,172.61,0.021575,0.42985,0.90264,98.461
> view matrix models
> #3,-0.86765,0.48419,-0.11289,118.38,-0.45783,-0.68959,0.56113,163.04,0.19384,0.53854,0.82,101.98
> view matrix models
> #3,0.81376,-0.37534,0.44376,107.66,-0.21651,0.5128,0.83076,175.82,-0.53937,-0.77211,0.33603,88.459
> view matrix models
> #3,0.64278,-0.75398,0.13542,106.47,-0.038665,0.14462,0.98873,169.63,-0.76507,-0.64078,0.063809,93.041
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.64278,-0.75398,0.13542,120.72,-0.038665,0.14462,0.98873,122.83,-0.76507,-0.64078,0.063809,109.45
> view matrix models
> #3,0.64278,-0.75398,0.13542,125,-0.038665,0.14462,0.98873,126.01,-0.76507,-0.64078,0.063809,110.11
> fitmap #3 inMap #1
Fit molecule PRO-120446-LC-1-107.pdb (#3) to map
cryosparc_P651_J24_006_volume_map.mrc (#1) using 817 atoms
average map value = 0.2922, steps = 76
shifted from previous position = 4.82
rotated from previous position = 21.9 degrees
atoms outside contour = 220, contour level = 0.1768
Position of PRO-120446-LC-1-107.pdb (#3) relative to
cryosparc_P651_J24_006_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.43655222 -0.80127769 0.40911637 119.05741592
-0.32884853 0.28115519 0.90155998 124.25784465
-0.83742509 -0.52811533 -0.14076007 110.94223559
Axis -0.73138727 0.63770043 0.24168332
Axis point 0.00000000 172.68837722 13.28666144
Rotation angle (degrees) 102.21181425
Shift along axis 18.97509006
> ui mousemode right select
> select clear
> open /Users/pfeliciano/Library/CloudStorage/OneDrive-
> GenerateBiomedicines/Documents/Projects/Outer-
> Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-108.pdb
Summary of feedback from opening
/Users/pfeliciano/Library/CloudStorage/OneDrive-
GenerateBiomedicines/Documents/Projects/Outer-
Loop/TheraSabDab/Structures/PRO-120446/docking/PRO-120446-LC-108.pdb
---
warning | Ignored bad PDB record found on line 871
Chain information for PRO-120446-LC-108.pdb #4
---
Chain | Description
B | No description available
Drag select of 112 residues
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-7.7056,0,1,0,93.523,0,0,1,102.08
> view matrix models #4,1,0,0,129.28,0,1,0,39.027,0,0,1,101.98
> view matrix models #4,1,0,0,137.39,0,1,0,102.27,0,0,1,106.39
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.90704,-0.35953,0.21913,141.8,0.17649,0.79717,0.57739,106.57,-0.38227,-0.48504,0.78652,110.31
> ui mousemode right select
> select clear
> select #4/B:108
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
===== 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 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: Z17G002HSLL/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 11881.61.3
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7.2 (23H311)
Kernel Version: Darwin 23.6.0
Time since boot: 7 days, 23 hours, 40 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 6 months ago
| 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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