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Opened 18 months ago
Closed 18 months ago
#15023 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-14.2.1-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 0x00000002d8ecb000 (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 0x00000001e08e5000 (most recent call first):
Garbage-collecting
File "", line 729 in _compile_bytecode
File "", line 1069 in get_code
File "", line 936 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "", line 241 in _call_with_frames_removed
File "", line 1234 in _handle_fromlist
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/special/__init__.py", line 780 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/interpolate/_interpolate.py", line 9 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/interpolate/__init__.py", line 167 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "", line 1206 in _gcd_import
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/importlib/__init__.py", line 126 in import_module
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/scipy/__init__.py", line 189 in __getattr__
File "", line 1231 in _handle_fromlist
File "/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/manipulations/register_shift.py", line 15 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/manipulations/__init__.py", line 12 in
File "", line 241 in _call_with_frames_removed
File "", line 940 in exec_module
File "", line 690 in _load_unlocked
File "", line 1149 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "", line 241 in _call_with_frames_removed
File "", line 1128 in _find_and_load_unlocked
File "", line 1178 in _find_and_load
File "/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/cmd/cmd.py", line 478 in register_isolde
File "/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/__init__.py", line 170 in register_command
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1286 in register_command
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 330 in _register_cmd
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 320 in cb
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 2158 in call
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 2227 in lazy_register
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 2579 in _find_command_name
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 2843 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 "/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/toolbar.py", line 19 in toolbar_command
File "/Users/ethancrofut/Library/Application Support/ChimeraX/1.7/lib/python/site-packages/chimerax/isolde/__init__.py", line 183 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, PIL._webp, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb (total: 68)
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"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 105557948104535\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600120000000-600140000000 [512.0M] rw-\/rwx SM=PRV ",
"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":28137},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 105557948104535\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO 600120000000-600140000000 [512.0M] rw-\/rwx SM=PRV ",
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{
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"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
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{
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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/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_alignedcoil_04162024.cxs
> format session
Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel
1.1, shown at level 0.129, step 1, values float32
opened ChimeraX session
> lighting flat
> close #3
> color #8 #a2ff35
> lighting full
> open /Users/ethancrofut/Downloads/EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb
Summary of feedback from opening
/Users/ethancrofut/Downloads/EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb
---
warning | Ignored bad PDB record found on line 38
DBREF XXXX A 1 380 UNP A0A7S3WEM8 A0A7S3WEM8_EMIHU 1 380
EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for hypothetical protein (A0A7S3WEM8) [more
info...]
Chain information for EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb #3
---
Chain | Description
A | hypothetical protein
> select add #3
2961 atoms, 2997 bonds, 380 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,392.59,0,1,0,220.83,0,0,1,72.867
> view matrix models #3,1,0,0,415.44,0,1,0,204.22,0,0,1,343.2
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.85059,-0.085848,0.51877,411.5,0.0030118,0.98736,0.15845,202.83,-0.52582,-0.13322,0.8401,346.58
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.85059,-0.085848,0.51877,400.15,0.0030118,0.98736,0.15845,202.02,-0.52582,-0.13322,0.8401,318.83
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.20162,-0.96988,-0.13665,412.42,0.93223,0.14721,0.33058,202.89,-0.3005,-0.19404,0.93383,317.78
> view matrix models
> #3,0.18607,-0.97739,-0.10044,412.17,0.92943,0.14194,0.3406,202.83,-0.31865,-0.15673,0.93483,317.61
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.18607,-0.97739,-0.10044,391.7,0.92943,0.14194,0.3406,275.88,-0.31865,-0.15673,0.93483,352.4
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.24072,-0.95371,-0.18025,392.18,0.80442,0.09212,0.58688,274.18,-0.5431,-0.28628,0.78936,354.94
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.24072,-0.95371,-0.18025,386.85,0.80442,0.09212,0.58688,276.47,-0.5431,-0.28628,0.78936,354.57
> view matrix models
> #3,0.24072,-0.95371,-0.18025,392.84,0.80442,0.09212,0.58688,270.61,-0.5431,-0.28628,0.78936,318.86
> view matrix models
> #3,0.24072,-0.95371,-0.18025,412.63,0.80442,0.09212,0.58688,276.28,-0.5431,-0.28628,0.78936,326.52
> ui mousemode right select
Drag select of 51 residues
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.24072,-0.95371,-0.18025,395.87,0.80442,0.09212,0.58688,271.51,-0.5431,-0.28628,0.78936,320.35
> view matrix models
> #3,0.24072,-0.95371,-0.18025,391.28,0.80442,0.09212,0.58688,278.87,-0.5431,-0.28628,0.78936,321.28
> ui tool show "Fit in Map"
> fitmap sel inMap #11
Fit molecule EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) to map
cryosparc_P9_J1527_map_sharp.mrc (#11) using 414 atoms
average map value = 0.1112, steps = 64
shifted from previous position = 2.88
rotated from previous position = 8.48 degrees
atoms outside contour = 246, contour level = 0.12883
Position of EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) relative to
cryosparc_P9_J1527_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.17748944 -0.94353524 -0.27971191 394.02099492
0.77654551 -0.04032251 0.62876956 274.31309170
-0.60454493 -0.32880898 0.72554124 324.85849974
Axis -0.47992137 0.16280054 0.86207393
Axis point 150.86045413 355.06826931 0.00000000
Rotation angle (degrees) 93.93621678
Shift along axis 135.61127000
> color #3 #dfdfdf
> select clear
> select add #3
2961 atoms, 2997 bonds, 380 residues, 1 model selected
> select #3/A:185
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #3/A:315
13 atoms, 11 bonds, 2 residues, 1 model selected
> select up
1606 atoms, 1621 bonds, 193 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.11897,-0.97295,-0.19805,393.57,0.81292,-0.019083,0.58206,274.54,-0.57009,-0.23025,0.78866,323.67
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.11897,-0.97295,-0.19805,385.26,0.81292,-0.019083,0.58206,279.52,-0.57009,-0.23025,0.78866,323.44
> view matrix models
> #3,0.11897,-0.97295,-0.19805,389.2,0.81292,-0.019083,0.58206,281.32,-0.57009,-0.23025,0.78866,325.83
> fitmap sel inMap #11
Fit molecule EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) to map
cryosparc_P9_J1527_map_sharp.mrc (#11) using 1606 atoms
average map value = 0.08517, steps = 268
shifted from previous position = 2.97
rotated from previous position = 9.8 degrees
atoms outside contour = 1105, contour level = 0.12883
Position of EHuxleyi_AF-A0A7S3WEM8-F1-model_v4.pdb (#3) relative to
cryosparc_P9_J1527_map_sharp.mrc (#11) coordinates:
Matrix rotation and translation
0.01522549 -0.95284833 -0.30306476 388.99981659
0.86750665 -0.13812812 0.47786278 285.41423032
-0.49719251 -0.27018639 0.82449919 327.57234644
Axis -0.37825851 0.09816263 0.92048063
Axis point 136.77681352 339.29774694 0.00000000
Rotation angle (degrees) 98.58066763
Shift along axis 182.39852067
> select clear
> show #3-8,12-13 target ab
> hide #3-8,12-13 target a
> cartoon #3-8,12-13
> show #9 models
> show #10 models
> color bfactor #3,4,5,6,7,8 palette alphafold
14952 atoms, 1848 residues, atom bfactor range 30 to 98.8
> hide #12 models
> hide #13 models
> windowsize 1000 500
> hide #3-10 target a
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> lighting full
> lighting soft
> lighting full
> hide #3 models
> show #6 models
> windowsize 1000 400
> hide #6 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #10 models
> hide #10 models
> windowsize 1000 500
> show #10 models
> hide #10 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #5 models
> hide #5 models
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> show #4 models
> hide #4 models
> show #5 models
> hide #5 models
> show #6 models
> hide #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #6 models
> hide #6 models
> show #9 models
> hide #9 models
> show #10 models
> hide #10 models
> show #10 models
> hide #10 models
> show #9 models
> hide #9 models
> show #8 models
> hide #8 models
> show #7 models
> hide #7 models
> show #3 models
> ui tool show "Side View"
> save "/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1.
> Research/Project #4 -
> TVMT/Johnson_TvMT/tvmt_figure_making/homology_AF_montage_04222024.cxs"
> close session
> open "/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1.
> Research/Project #4 -
> TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs" format
> session
No such file/path: /Users/ethancrofut/Google Drive/My Drive/3.
Extracurricular/1. Research/Project #4 -
TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs
> open "/Users/ethancrofut/Google Drive/My Drive/3. Extracurricular/1.
> Research/Project #4 -
> TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs" format
> session
No such file/path: /Users/ethancrofut/Google Drive/My Drive/3.
Extracurricular/1. Research/Project #4 -
TVMT/Johnson_TvMT/tvmt_figure_making/homology_kink_04212024.cxs
> open /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024-0.cxs
> format session
No such file/path: /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
ecrofut@g.ucla.edu/.shortcut-targets-by-
id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024-0.cxs
> open /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_04162024-0.cxs
> format session
No such file/path: /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
ecrofut@g.ucla.edu/.shortcut-targets-by-
id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_04162024-0.cxs
> open /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024.cxs
> format session
No such file/path: /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
ecrofut@g.ucla.edu/.shortcut-targets-by-
id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology_figure_kink_04192024.cxs
> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/homology_cxs/homology_figure_kink_04192024-0.cxs"
Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel
1.1, shown at level 0.129, step 1, values float32
opened ChimeraX session
> ui mousemode right select
Drag select of 437 residues, 38 atoms, 32 bonds
> hide sel target ab
> select clear
> windowsize 1000 500
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/superimposition_tbinding_04232024.tif" width 1000 height 500
> supersample 3 transparentBackground true
> select #2/F:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/F:203-210
75 atoms, 74 bonds, 8 residues, 1 model selected
> hide #12 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/F #13/F
Alignment identifier is 1
> select #2/F:203 #13/F:203
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:203-207 #13/F:203-207
88 atoms, 86 bonds, 10 residues, 2 models selected
1 [ID: 1] region 2 chains [189-193] RMSD: 115.258
> select #2/F:202 #13/F:202
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:202-203 #13/F:202-203
32 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [188-189] RMSD: 113.455
> show (#13 & sel) target ab
> select #2/F:205 #13/F:205
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:205-206 #13/F:205-206
38 atoms, 36 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [191-192] RMSD: 117.252
> show (#13 & sel) target ab
> select #2/F:212 #13/F:212
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:212-213 #13/F:212-213
30 atoms, 28 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [198-199] RMSD: 119.137
> show (#13 & sel) target ab
> select #2/F:218 #13/F:218
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #2/F:218 #13/F:218
24 atoms, 24 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [204] RMSD: 121.553
> show (#13 & sel) target ab
> select #2/F:220 #13/F:220
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/F:220-221 #13/F:220-221
28 atoms, 26 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [206-207] RMSD: 118.698
> show (#13 & sel) target ab
> view name tbinding
> select #2/F:225 #13/F:225
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #2/F:225 #13/F:225
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [211] RMSD: 120.382
> show (#13 & sel) target ab
> select #2/F:231 #13/F:231
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:231-232 #13/F:231-232
34 atoms, 32 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [217-218] RMSD: 117.841
> show (#13 & sel) target ab
> select #2/F:235 #13/F:235
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/F:235-236 #13/F:235-236
36 atoms, 34 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [221-222] RMSD: 117.727
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/fap35only_tbdingin_04232024.tif" width 1000 height 500 supersample 3
> transparentBackground true
> close session
> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/homology_cxs/homology_figure_N_04192024.cxs"
Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel
1.1, shown at level 0.129, step 1, values float32
opened ChimeraX session
> select #12/B:149
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> view list
Named views: N_aromatic, tubulin_binding_motif
> view N_aromatic
> windowsize 600 600
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/superimposition_N_04232024.tif" width 800 height 800 supersample 3
> transparentBackground true
> color #3 #dfdfdf
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/superimposition_N_04232024.tif" width 800 height 800 supersample 3
> transparentBackground true
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/homology_cxs/homology_figure_N_04232024.cxs"
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #12 models
> select #13/F:103
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/fap35only_N_04232024.tif" width 800 height 800 supersample 3
> transparentBackground true
> close session
> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/homology_cxs/homology_figure_kink_04192024-0.cxs" format session
Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel
1.1, shown at level 0.129, step 1, values float32
opened ChimeraX session
> hide #3-8,12-13 target a
> windowsize 1000 500
> select clear
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #3 models
> hide #4 models
> hide #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #2/F #13/F
Alignment identifier is 1
> select #2/F:56-69,83-98,103-184,201-214,218-304
> #13/F:56-69,83-98,103-184,201-214,218-304
3542 atoms, 3560 bonds, 426 residues, 2 models selected
> select #2/F:202 #13/F:202
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:202-203 #13/F:202-203
32 atoms, 30 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [188-189] RMSD: 113.455
> show (#13 & sel) target ab
> select #2/F:205 #13/F:205
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:205-206 #13/F:205-206
38 atoms, 36 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [191-192] RMSD: 117.252
> show (#13 & sel) target ab
> select #2/F:212 #13/F:212
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:212-213 #13/F:212-213
30 atoms, 28 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [198-199] RMSD: 119.137
> show (#13 & sel) target ab
> select #2/F:218 #13/F:218
24 atoms, 24 bonds, 2 residues, 2 models selected
> select #2/F:218 #13/F:218
24 atoms, 24 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [204] RMSD: 121.553
> show (#13 & sel) target ab
> select #2/F:220 #13/F:220
18 atoms, 16 bonds, 2 residues, 2 models selected
> select #2/F:220-221 #13/F:220-221
28 atoms, 26 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [206-207] RMSD: 118.698
> show (#13 & sel) target ab
> select #2/F:225 #13/F:225
20 atoms, 20 bonds, 2 residues, 2 models selected
> select #2/F:225 #13/F:225
20 atoms, 20 bonds, 2 residues, 2 models selected
1 [ID: 1] region 2 chains [211] RMSD: 120.382
> show (#13 & sel) target ab
> select #2/F:231 #13/F:231
16 atoms, 14 bonds, 2 residues, 2 models selected
> select #2/F:231-232 #13/F:231-232
34 atoms, 32 bonds, 4 residues, 2 models selected
1 [ID: 1] region 2 chains [217-218] RMSD: 117.841
> show (#13 & sel) target ab
> select clear
> windowsize 1000 500
> view list
Named views: tbinding_04192024, tubulin_binding_motif
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/fap35only_tbdingin_04232024-0.tif" width 1000 height 500 supersample
> 3 transparentBackground true
> show #8 models
> show #7 models
> show #6 models
> show #5 models
> show #4 models
> show #3 models
> show #12 models
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/superimposition_tbinding_04232024-0.tif" width 1000 height 500
> supersample 3 transparentBackground true
> hide #3-8,12-13 target a
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/superimposition_tbinding_04232024-0.tif" width 1000 height 500
> supersample 3 transparentBackground true
> windowsize 1000 500
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> hide #7 models
> hide #8 models
> hide #12 models
> close session
> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/homology_cxs/homology_figure_N_04192024.cxs" format session
Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel
1.1, shown at level 0.129, step 1, values float32
opened ChimeraX session
> close session
> open "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/homology_cxs/homology_figure_kink_04192024-0.cxs" format session
Opened cryosparc_P9_J1527_map_sharp.mrc as #11, grid size 640,640,640, pixel
1.1, shown at level 0.129, step 1, values float32
opened ChimeraX session
> hide #12 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> hide #3 models
> select #13/F:203
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/F:202
16 atoms, 14 bonds, 2 residues, 1 model selected
> hide sel target a
> select clear
Drag select of 16 atoms, 10 residues, 16 bonds
> show sel target ab
> undo
> select #13/F:208
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #13/F:206
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel target ab
> select #13/F:208
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select #13/F:206
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel target a
> select clear
> save "/Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/homology
> figure/fap35_only_tbinding_closeup_04242024.tif" width 1000 height 500
> supersample 3 transparentBackground true
> close session
> open /Users/ethancrofut/Library/CloudStorage/GoogleDrive-
> ecrofut@g.ucla.edu/.shortcut-targets-by-
> id/10G9qsWdpws6WuAuYr7FnfkwnO77Ili94/Johnson_TvMT/tvmt_figure_making/MIPS_fit_figure/supplemental_mip_figures.cxs
Opened 16nm_Bmap_UD2_sharp_J1506.mrc as #1, grid size 640,640,640, pixel 1.1,
shown at level 0.0929, step 1, values float32
opened ChimeraX session
> select clear
> hide #!1 models
> show #!1 models
> volume copy #1
Opened 16nm_Bmap_UD2_sharp_J1506.mrc copy as #3, grid size 640,640,640, pixel
1.1, shown at step 1, values float32
> combine #2
> color #3 darkgrey models
> hide #2 models
> hide #4 models
> show #4 models
> clipper associate #3 toModel #4
Opened 16nm_Bmap_UD2_sharp_J1506.mrc copy as #3.1.1.1, grid size 640,640,640,
pixel 1.1, shown at level 0.143, step 1, values float32
===== 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
OpenGL renderer: Apple M1
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 Air
Model Identifier: MacBookAir10,1
Model Number: Z127000FLLL/A
Chip: Apple M1
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 108 days, 20 hours, 40 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 7
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2714H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
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 |
Note:
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