![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 15 months ago
Closed 15 months ago
#15853 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.6-x86_64-i386-64bit
ChimeraX Version: 1.8rc202405312319 (2024-05-31 23:19:45 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff855d9c700 (most recent call first):
File "/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 307 in event_loop
File "/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, PIL._webp (total: 62)
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{
"uptime" : 820000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,1",
"coalitionID" : 239253,
"osVersion" : {
"train" : "macOS 13.6",
"build" : "22G120",
"releaseType" : "User"
},
"captureTime" : "2024-08-30 16:32:33.8544 +0200",
"incident" : "50D1148B-45E9-4FEA-BCB3-C98E4FEB163D",
"pid" : 91541,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-30 11:51:34.8715 +0200",
"procStartAbsTime" : 818366004935414,
"procExitAbsTime" : 825751541130904,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8-rc2024.05.31.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3DB4FC6A-27E9-56B8-95F0-FC21B148075B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "407E303B-BF04-4FEE-B7F6-8A8451CA77F1",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 1821,
"bridgeVersion" : {"build":"21P365","train":"8.0"},
"sleepWakeUUID" : "D551DAD9-A913-4929-B4DB-EE7884068F42",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4493860864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10bdae000-10bdb2000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":91541},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4493860864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10bdae000-10bdb2000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.29_Modelpaper.cxs
> format session
Opened cryosparc_P110_J215_002_volume_mask_refine.mrc as #1, grid size
440,440,440, pixel 0.926, shown at level 5e-05, step 1, values float32
Opened Cryo_Rod_volume_map as #4, grid size 440,440,440, pixel 0.926, shown at
level 0.0395, step 2, values float32
Opened Cryo_Coiled_coil as #5, grid size 256,256,256, pixel 1.59, shown at
level 0.263, step 1, values float32
Opened Cryo_Coiled_coil x flip as #6, grid size 256,256,256, pixel 1.59, shown
at level 0.259, step 1, values float32
Opened Cryo_Rod_Aligned_AF3#8_Volume as #7, grid size 440,440,440, pixel
0.926, shown at level 0.041, step 1, values float32
Opened Cryo_Rod_Aligned_Xflip_AF3#10_Volume as #9, grid size 440,440,440,
pixel 0.926, shown at level 0.0388, step 1, values float32
opened ChimeraX session
> combine #3
> select add #11
9444 atoms, 9660 bonds, 1194 residues, 2 models selected
> select subtract #10
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> show sel cartoons
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.71372,-0.60391,0.3548,187.12,-0.68351,0.71118,-0.16445,331.03,-0.15302,-0.35988,-0.92037,145.56
> view matrix models
> #11,-0.71372,-0.60391,0.3548,208.37,-0.68351,0.71118,-0.16445,337.08,-0.15302,-0.35988,-0.92037,36.383
> ui mousemode right select
> select subtract #11
Nothing selected
Drag select of 22 residues
> delete atoms sel
> delete bonds sel
Drag select of 2 residues
Drag select of 24 residues
> delete atoms sel
> delete bonds sel
Drag select of 22 residues
> delete atoms sel
> delete bonds sel
> select add #11
4240 atoms, 4332 bonds, 529 residues, 1 model selected
> ui mousemode right select
> ui mousemode right "translate selected models"
> view matrix models
> #11,-0.71372,-0.60391,0.3548,408.05,-0.68351,0.71118,-0.16445,367.04,-0.15302,-0.35988,-0.92037,206.32
> ui mousemode right select
> select clear
Drag select of 5 residues
> select add #11
4240 atoms, 4332 bonds, 529 residues, 1 model selected
> select subtract #11
Nothing selected
> close #3
> close session
> open
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.29_Modelpaper.cxs
> format session
Opened cryosparc_P110_J215_002_volume_mask_refine.mrc as #1, grid size
440,440,440, pixel 0.926, shown at level 5e-05, step 1, values float32
Opened Cryo_Rod_volume_map as #4, grid size 440,440,440, pixel 0.926, shown at
level 0.0395, step 2, values float32
Opened Cryo_Coiled_coil as #5, grid size 256,256,256, pixel 1.59, shown at
level 0.263, step 1, values float32
Opened Cryo_Coiled_coil x flip as #6, grid size 256,256,256, pixel 1.59, shown
at level 0.259, step 1, values float32
Opened Cryo_Rod_Aligned_AF3#8_Volume as #7, grid size 440,440,440, pixel
0.926, shown at level 0.041, step 1, values float32
Opened Cryo_Rod_Aligned_Xflip_AF3#10_Volume as #9, grid size 440,440,440,
pixel 0.926, shown at level 0.0388, step 1, values float32
opened ChimeraX session
> combine #8
> select add #11
9444 atoms, 9660 bonds, 1194 residues, 2 models selected
> select subtract #10
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select up
23610 atoms, 24150 bonds, 2985 residues, 17 models selected
> select up
23610 atoms, 24150 bonds, 2985 residues, 24 models selected
> close #11
> open
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/OR1_a26ff_Alphafold/OR1_a26ff_scores_rank_004_alphafold2_multimer_v3_model_1_seed_000.json
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8-rc2024.05.31.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 130, in
if hasattr(m, 'filename') and dirname(m.filename) == dirname(path)]
^^^^^^^^^^^^^^^^^^^
File "", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
> open
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/OR1_a26ff_Alphafold/OR1_a26ff_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb
Chain information for
OR1_a26ff_unrelaxed_rank_004_alphafold2_multimer_v3_model_1_seed_000.pdb #11
---
Chain | Description
A B C | No description available
> open
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/OR1_a26ff_Alphafold/OR1_a26ff_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb
Chain information for
OR1_a26ff_unrelaxed_rank_001_alphafold2_multimer_v3_model_2_seed_000.pdb #12
---
Chain | Description
A B C | No description available
> select subtract #1
18888 atoms, 19320 bonds, 2388 residues, 20 models selected
> select subtract #2
14166 atoms, 14490 bonds, 1791 residues, 19 models selected
> select subtract #3
9444 atoms, 9660 bonds, 1194 residues, 15 models selected
> select subtract #4
9444 atoms, 9660 bonds, 1194 residues, 10 models selected
> select subtract #5
9444 atoms, 9660 bonds, 1194 residues, 8 models selected
> select subtract #6
9444 atoms, 9660 bonds, 1194 residues, 6 models selected
> select subtract #7
9444 atoms, 9660 bonds, 1194 residues, 4 models selected
> select subtract #8
4722 atoms, 4830 bonds, 597 residues, 3 models selected
> select subtract #9
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select subtract #10
Nothing selected
> select add #11
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #11,1,0,0,-116.57,0,1,0,-44.183,0,0,1,-11.013
> select subtract #11
Nothing selected
> select add #11
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> view matrix models #11,1,0,0,-107.99,0,1,0,-28.469,0,0,1,1.6822
> view matrix models
> #11,0.73417,0.097041,-0.672,-104.44,0.51687,-0.72166,0.46048,-9.5469,-0.44027,-0.68541,-0.57998,21.823
> view matrix models
> #11,0.6985,0.18244,-0.69196,-105.35,0.4822,-0.83447,0.26675,-6.763,-0.52876,-0.51998,-0.67085,20.429
> close #11 #12
> select add #9
2 models selected
> select subtract #9
Nothing selected
> select add #10
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> view matrix models
> #10,0.020416,-0.03601,-0.99914,238.41,0.79209,0.61038,-0.0058134,222.74,0.61007,-0.79129,0.040985,-102.28
> show sel cartoons
> ui mousemode right select
Drag select of 20 residues
> select clear
Drag select of 21 residues
> delete atoms sel
> delete bonds sel
Drag select of 12 residues
> select clear
Drag select of 34 residues
> select clear
Drag select of 21 residues
> delete atoms sel
> delete bonds sel
> select clear
Drag select of 18 residues
> delete atoms sel
> delete bonds sel
Drag select of 4 residues
> delete atoms sel
> delete bonds sel
> select add #10
4269 atoms, 4362 bonds, 533 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> transparency (#!10 & sel) 80
> hide sel cartoons
> color (#!10 & sel) light gray
> show sel cartoons
> hide sel surfaces
> undo
> show sel surfaces
> rename #10 Model
> select clear
> ui mousemode right "translate selected models"
> select add #10
4269 atoms, 4362 bonds, 533 residues, 1 model selected
> view matrix models
> #10,0.020416,-0.03601,-0.99914,268.51,0.79209,0.61038,-0.0058134,291.87,0.61007,-0.79129,0.040985,-71.204
> view matrix models
> #10,0.020416,-0.03601,-0.99914,265.05,0.79209,0.61038,-0.0058134,284.55,0.61007,-0.79129,0.040985,-74.86
> view matrix models
> #10,0.60627,-0.15861,-0.77928,265.75,0.77022,0.36108,0.52573,285.86,0.198,-0.91895,0.34107,-74.224
> view matrix models
> #10,0.76801,-0.094854,-0.63338,268.08,0.63622,0.2264,0.73754,286.02,0.073436,-0.96941,0.23422,-75.984
> select subtract #10
3 models selected
> select add #10
4269 atoms, 4362 bonds, 533 residues, 1 model selected
> select subtract #10
3 models selected
> select add #9
2 models selected
> select subtract #9
Nothing selected
> select add #3
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select subtract #3
3 models selected
> select add #3
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select subtract #3
3 models selected
> select add #2
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> view matrix models
> #2,-0.09195,0.31094,-0.94597,151.18,0.7664,0.62862,0.13213,476.46,0.63575,-0.71285,-0.29611,13.95
> select add #10
8991 atoms, 9192 bonds, 1130 residues, 5 models selected
> select subtract #2
4269 atoms, 4362 bonds, 533 residues, 7 models selected
> view matrix models
> #10,0.76801,-0.094854,-0.63338,371.52,0.63622,0.2264,0.73754,314.87,0.073436,-0.96941,0.23422,269.65
> view matrix models
> #10,0.76801,-0.094854,-0.63338,368.7,0.63622,0.2264,0.73754,313.96,0.073436,-0.96941,0.23422,260.33
> select subtract #10
3 models selected
> select add #3
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select add #2
9444 atoms, 9660 bonds, 1194 residues, 5 models selected
> select subtract #3
4722 atoms, 4830 bonds, 597 residues, 7 models selected
> view matrix models
> #2,-0.09195,0.31094,-0.94597,174.09,0.7664,0.62862,0.13213,331.4,0.63575,-0.71285,-0.29611,-100.79
> select add #10
8991 atoms, 9192 bonds, 1130 residues, 5 models selected
> select subtract #2
4269 atoms, 4362 bonds, 533 residues, 7 models selected
> view matrix models
> #10,0.76801,-0.094854,-0.63338,210.55,0.63622,0.2264,0.73754,350.97,0.073436,-0.96941,0.23422,338.6
> view matrix models
> #10,0.78403,-0.070115,-0.61675,211.02,0.60046,0.33748,0.72495,352.17,0.15731,-0.93872,0.30669,339.74
> view matrix models
> #10,0.78403,-0.070115,-0.61675,208.97,0.60046,0.33748,0.72495,359.37,0.15731,-0.93872,0.30669,329.86
> view matrix models
> #10,0.78299,-0.071937,-0.61787,208.93,0.60293,0.33206,0.7254,359.31,0.15298,-0.94051,0.30337,329.8
> view matrix models
> #10,0.79137,-0.05649,-0.60872,209.21,0.5815,0.3768,0.72103,359.79,0.18863,-0.92457,0.33104,330.29
> view matrix models
> #10,0.79137,-0.05649,-0.60872,210.54,0.5815,0.3768,0.72103,361.29,0.18863,-0.92457,0.33104,333.04
> hide #8 models
> hide #!9 models
> hide #7.1 models
> hide #!7 models
> hide #6.1 models
> hide #!6 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> view matrix models
> #10,0.79137,-0.05649,-0.60872,210.68,0.5815,0.3768,0.72103,356.1,0.18863,-0.92457,0.33104,328.4
> view matrix models
> #10,0.53504,0.047901,-0.84347,205.71,0.71625,0.50373,0.48295,355,0.44801,-0.86253,0.23521,330.01
> view matrix models
> #10,0.49775,0.11104,-0.86018,206.32,0.78904,0.35378,0.50225,353.39,0.36009,-0.92871,0.088484,327.83
> view matrix models
> #10,-0.17025,0.23652,-0.95659,206.85,0.73205,0.6802,0.037899,353.32,0.65964,-0.69382,-0.28895,327.49
> view matrix models
> #10,-0.070496,0.2364,-0.96909,206.97,0.76628,0.63482,0.099116,353.35,0.63863,-0.73561,-0.2259,327.45
> select subtract #10
3 models selected
> hide #!10 models
> combine #3
> close session
> open
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.28_Model_Yoan.cxs
Opened cryosparc_P110_J215_002_volume_map.mrc as #2, grid size 440,440,440,
pixel 0.926, shown at level 0.0687, step 2, values float32
Opened map_core.mrc as #10, grid size 256,256,256, pixel 1.59, shown at level
0.263, step 1, values float32
Opened cryosparc_P110_J215_002_volume_mask_refine.mrc as #1, grid size
440,440,440, pixel 0.926, shown at level 5e-05, step 1, values float32
opened ChimeraX session
> show #!1 models
> select add #2
2 models selected
> select subtract #2
Nothing selected
> rename #1 CryoEM_rod_mask
> rename #2 CryoEM_rod_volume
> hide #4 models
> show #4 models
> rename #4 A
> rename #4 CryoEM_rod_AF3
> select add #9
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select subtract #9
Nothing selected
> rename #10 CryoEM_CC_volume
> rename #10 id #5
> rename #9 CryoEM_CC_AF3
> rename #9 id #6
> combine CryoEM_rod_AF3
Expected a keyword
> rename #4 id #3
> rename #5 id #4
> rename #6 id #5
> combine #3
> select add #6
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> view matrix models
> #6,-0.44116,-0.57715,0.68722,107,-0.84317,0.52879,-0.097174,367.64,-0.30731,-0.62232,-0.71992,116.34
> view matrix models
> #6,-0.44116,-0.57715,0.68722,107.75,-0.84317,0.52879,-0.097174,431.7,-0.30731,-0.62232,-0.71992,74.632
> ui mousemode right select
> select clear
Drag select of 24 residues
> delete atoms sel
> delete bonds sel
Drag select of 17 residues
> select clear
Drag select of 16 residues
> select clear
Drag select of 21 residues
> delete atoms sel
> delete bonds sel
Drag select of 24 residues
> delete atoms sel
> delete bonds sel
> rename #6 AF3_surface
> name DUF3669 #6:10-93
> name KRAB #6:109-184
> color #4 light gray
> color DUF3669 medium purple
> color KRAB steel blue
> color #6 light gray
> color DUF3669 medium purple
> color KRAB steel blue
> color DUF3669 #D8CEE6
> color DUF3669 #9167AC
> color DUF3669 #D8CEE6
> color DUF3669 #74459B
> color DUF3669 #9F82BC
> color KRAB #A2ADBA
> color KRAB #8898A9
> combine #6
> select add #7
4238 atoms, 4329 bonds, 528 residues, 1 model selected
Drag select of 30 residues
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.44116,-0.57715,0.68722,163.03,-0.84317,0.52879,-0.097174,409.22,-0.30731,-0.62232,-0.71992,51.993
> select subtract #7
Nothing selected
> color #7.1 #BFA1C3
> color #7.2 #9167AC
> color #7.3 #64417F
> split #7
Split copy of AF3_surface (#7) into 3 models
Chain information for copy of AF3_surface A #7.1
---
Chain | Description
A | No description available
Chain information for copy of AF3_surface B #7.2
---
Chain | Description
B | No description available
Chain information for copy of AF3_surface C #7.3
---
Chain | Description
C | No description available
> split #6
Split AF3_surface (#6) into 3 models
Chain information for AF3_surface A #6.1
---
Chain | Description
A | No description available
Chain information for AF3_surface B #6.2
---
Chain | Description
B | No description available
Chain information for AF3_surface C #6.3
---
Chain | Description
C | No description available
> select add #5
4722 atoms, 4830 bonds, 597 residues, 1 model selected
> select subtract #5
Nothing selected
> split #5
Split CryoEM_CC_AF3 (#5) into 3 models
Chain information for CryoEM_CC_AF3 A #5.1
---
Chain | Description
A | No description available
Chain information for CryoEM_CC_AF3 B #5.2
---
Chain | Description
B | No description available
Chain information for CryoEM_CC_AF3 C #5.3
---
Chain | Description
C | No description available
> split #3
Split CryoEM_rod_AF3 (#3) into 3 models
Chain information for CryoEM_rod_AF3 A #3.1
---
Chain | Description
A | No description available
Chain information for CryoEM_rod_AF3 B #3.2
---
Chain | Description
B | No description available
Chain information for CryoEM_rod_AF3 C #3.3
---
Chain | Description
C | No description available
> split #2
> rename #6 AF3_DK_surface
> rename #7 AF3_TRIMER_surface
> color #7.1 #BFA1C3
> color #7.2 #9167AC
> color #7.3 #64417F
> select add #7
4238 atoms, 4329 bonds, 528 residues, 4 models selected
> view matrix models #7,1,0,0,-74.09,0,1,0,82.431,0,0,1,64.257
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> select subtract #7
3 models selected
> select add #7.1
1406 atoms, 1436 bonds, 175 residues, 1 model selected
> select add #7
4238 atoms, 4329 bonds, 528 residues, 5 models selected
> select subtract #7
3 models selected
> select add #6
4238 atoms, 4329 bonds, 528 residues, 4 models selected
> show sel surfaces
> transparency (#!6.1-3 & sel) 90
> ui mousemode right select
> select clear
> select add #7
4238 atoms, 4329 bonds, 528 residues, 4 models selected
> ui mousemode right "translate selected models"
> view matrix models #7,1,0,0,-75.07,0,1,0,83.671,0,0,1,61.184
> volume flip #2 axis x
Opened CryoEM_rod_volume x flip as #8, grid size 440,440,440, pixel 0.926,
shown at step 1, values float32
> volume flip #8 axis x
Opened CryoEM_rod_volume x flip x flip as #9, grid size 440,440,440, pixel
0.926, shown at step 1, values float32
> show #!8 models
> hide #!1 models
> show #!2 models
> hide #!2 models
> color #8 #ffb24b75 models
> color #8 #1d62eaff models
> select subtract #7
3 models selected
> select add #8
2 models selected
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-130.66,-0.87083,0.48516,0.079178,236.14,-0.48372,-0.87441,0.03776,235.18
> select subtract #8
Nothing selected
> select add #9
2 models selected
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-167.69,-0.87083,0.48516,0.079178,314.03,-0.48372,-0.87441,0.03776,280.38
> rename #9 CryoEM_rod_volume
> rename #8 CryoEM_rod_volume_Xflip
> rename #9 CryoEM_rod_volume_2
> rename #8 id #10
> rename #9 id #8
> rename #10 id #9
> ui mousemode right select
> select clear
> select add #8
2 models selected
> select add #9
4 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-164.77,-0.87083,0.48516,0.079178,399.52,-0.48372,-0.87441,0.03776,301.28,#9,0.087553,-0.0054174,0.99615,-127.74,-0.87083,0.48516,0.079178,321.64,-0.48372,-0.87441,0.03776,256.08
> select subtract #8
2 models selected
> select subtract #9
Nothing selected
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!7 models
> hide #!8 models
> hide #!9 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> select add #1
3 models selected
> select add #2
5 models selected
> select add #3
4722 atoms, 4830 bonds, 597 residues, 9 models selected
> select add #4
4722 atoms, 4830 bonds, 597 residues, 11 models selected
> select add #5
9444 atoms, 9660 bonds, 1194 residues, 15 models selected
> view matrix models
> #2,0.087553,-0.0054174,0.99615,-126.95,-0.87083,0.48516,0.079178,669.46,-0.48372,-0.87441,0.03776,739.35,#1,0.13568,0.017664,0.9906,-141.79,-0.87217,0.47646,0.11096,662.72,-0.47002,-0.87902,0.080052,729.58,#4,1,0,0,18.98,0,1,0,328.98,0,0,1,203.48,#5,1,0,0,18.98,0,1,0,328.98,0,0,1,203.48,#3,1,0,0,18.98,0,1,0,328.98,0,0,1,203.48
> view matrix models
> #2,0.087553,-0.0054174,0.99615,-304.16,-0.87083,0.48516,0.079178,895.58,-0.48372,-0.87441,0.03776,904.19,#1,0.13568,0.017664,0.9906,-319,-0.87217,0.47646,0.11096,888.85,-0.47002,-0.87902,0.080052,894.42,#4,1,0,0,-158.23,0,1,0,555.1,0,0,1,368.32,#5,1,0,0,-158.23,0,1,0,555.1,0,0,1,368.32,#3,1,0,0,-158.23,0,1,0,555.1,0,0,1,368.32
> hide #!1 models
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> select subtract #1
9444 atoms, 9660 bonds, 1194 residues, 12 models selected
> select subtract #2
9444 atoms, 9660 bonds, 1194 residues, 10 models selected
> select subtract #3
4722 atoms, 4830 bonds, 597 residues, 6 models selected
> select subtract #4
4722 atoms, 4830 bonds, 597 residues, 4 models selected
> select subtract #5
Nothing selected
> show #!6 models
> show #!7 models
> show #!8 models
> show #!9 models
> select add #8
2 models selected
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-118.06,-0.87083,0.48516,0.079178,412.77,-0.48372,-0.87441,0.03776,310.17
> select add #9
4 models selected
> select subtract #8
2 models selected
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-93.297,-0.87083,0.48516,0.079178,335.93,-0.48372,-0.87441,0.03776,265.89
> volume #9 level 0.05334
> volume #8 level 0.0533
> select add #8
4 models selected
> select subtract #9
2 models selected
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-407.88,-0.87083,0.48516,0.079178,445.46,-0.48372,-0.87441,0.03776,312.07
> select subtract #8
Nothing selected
> select add #9
2 models selected
> hide #!8 models
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-131.66,-0.87083,0.48516,0.079178,421.98,-0.48372,-0.87441,0.03776,294.72
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-132.54,-0.87083,0.48516,0.079178,431.18,-0.48372,-0.87441,0.03776,300.33
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-130,-0.87083,0.48516,0.079178,417.09,-0.48372,-0.87441,0.03776,310.95
> show #!8 models
> select add #8
4 models selected
> select subtract #9
2 models selected
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-158.65,-0.87083,0.48516,0.079178,396.29,-0.48372,-0.87441,0.03776,172.41
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-122.22,-0.87083,0.48516,0.079178,340.88,-0.48372,-0.87441,0.03776,272.5
> select subtract #8
Nothing selected
> select add #9
2 models selected
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-205.05,-0.87083,0.48516,0.079178,390.81,-0.48372,-0.87441,0.03776,314.95
> select add #8
4 models selected
> select subtract #9
2 models selected
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-127.11,-0.87083,0.48516,0.079178,409.09,-0.48372,-0.87441,0.03776,326.22
> hide #!9 models
> volume #8 level 0.03045
> surface dust #8 size 9.26
> show #!9 models
> select subtract #8
Nothing selected
> select add #9
2 models selected
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-275.85,-0.87083,0.48516,0.079178,384.65,-0.48372,-0.87441,0.03776,324.26
> select subtract #9
Nothing selected
> select add #8
2 models selected
> view matrix models
> #8,0.087553,-0.0054174,0.99615,-128.68,-0.87083,0.48516,0.079178,415,-0.48372,-0.87441,0.03776,314.07
> select subtract #8
Nothing selected
> select add #9
2 models selected
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-221.68,-0.87083,0.48516,0.079178,251.45,-0.48372,-0.87441,0.03776,227.98
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-223.3,-0.87083,0.48516,0.079178,251.24,-0.48372,-0.87441,0.03776,218.02
> view matrix models
> #9,0.087553,-0.0054174,0.99615,-219.1,-0.87083,0.48516,0.079178,201.87,-0.48372,-0.87441,0.03776,204.77
> hide #!6 models
> show #!6 models
> select add #8
4 models selected
> select subtract #8
2 models selected
> select add #8
4 models selected
> select subtract #9
2 models selected
> color #8 #ebebebff models
> color #8 white models
> color #8 #ebebebff models
> color #8 #d6d6d6ff models
> color #8 silver models
> color #8 #d783ffff models
> color #8 #ff85ffff models
> color #8 #bfa1c3ff models
> transparency #8.1 70
> lighting flat
> lighting full
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> ui tool show "Side View"
> select add #8
3 models selected
> select subtract #8
Nothing selected
> save
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/2024.05.29_Modelpaper_2.cxs
No map chosen to save
> save
> /Users/rosspopoff/Dropbox/Trono_Lab/37-FindingDUF3669/9-PTPSP_data/cryosparc/blo.tif
> width 2000 height 1443 supersample 3 transparentBackground true
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8rc202405312319 (2024-05-31)
© 2016-2024 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 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,1
Processor Name: 6-Core Intel Core i9
Processor Speed: 2.9 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.6 (22G120)
Kernel Version: Darwin 22.6.0
Time since boot: 20 days, 14 hours, 47 minutes
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: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Radeon Pro 560X:
Chipset Model: Radeon Pro 560X
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c2
ROM Revision: 113-C980AL-075
VBIOS Version: 113-C97501U-005
EFI Driver Version: 01.A1.075
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 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: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57
ChimeraX-AtomicLibrary: 14.0.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8rc202405312319
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
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: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
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: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.16
ChimeraX-ModelPanel: 1.5
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: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.4
ChimeraX-PDB: 2.7.5
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: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
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-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
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: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.45
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
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: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4
traitlets: 5.14.2
typing-extensions: 4.12.1
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 15 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 15 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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Mac Qt 6.6 bug, crash in displayConfigFinalizedProc. Either plugging in or unplugging display or waking from sleep.