![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#16324 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-13.6.9-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00007ff85a55a7c0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.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.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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, 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 (total: 61)
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{
"uptime" : 6800000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "iMac18,2",
"coalitionID" : 759849,
"osVersion" : {
"train" : "macOS 13.6.9",
"build" : "22G830",
"releaseType" : "User"
},
"captureTime" : "2024-11-15 17:03:58.4280 -0800",
"incident" : "BB80018A-C757-43C5-ABD2-9FD03FCBD389",
"pid" : 63741,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-11-14 10:39:05.1212 -0800",
"procStartAbsTime" : 6718130813024319,
"procExitAbsTime" : 6827621441029992,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"3E6B1F6F-15B1-5D0C-9573-1FCC44DF3DDD","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "0709470B-9D72-36E7-9433-8A4C0BF2048B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4316504064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10148a000-10148e000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":63741},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4316504064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10148a000-10148e000 [ 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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"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
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"name" : "libdispatch.dylib"
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"base" : 140703513300992,
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"size" : 4837360,
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"path" : "\/usr\/lib\/libc++.1.dylib",
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"legacyInfo" : {
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"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
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},
"logWritingSignature" : "e4af7061f6f162f4114c6826e7fd3731a40ee6e7",
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}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> volume step 1
Error running startup command 'volume step 1': No volumes specified
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Local
> Refinement/Fit Hrr25 in J106 map.cxs" format session
Opened cryosparc_P49_J106_007_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.73, shown at level 0.101, step 1, values float32
opened ChimeraX session
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Homo
> Refinement/J93/cryosparc_P49_J93_004_volume_map.mrc" format mrc
Opened cryosparc_P49_J93_004_volume_map.mrc as #6, grid size 256,256,256,
pixel 1.73, shown at level 0.263, step 1, values float32
> color #1 #bf80ae8e models
> close session
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Local
> Refinement/J106/cryosparc_P49_J106_007_volume_map.mrc"
Opened cryosparc_P49_J106_007_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.73, shown at level 0.0215, step 1, values float32
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/EMData/230701TuSC110+Hrr25/csparc/Homo
> Refinement/J93/cryosparc_P49_J93_004_volume_map.mrc"
Opened cryosparc_P49_J93_004_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.73, shown at level 0.263, step 1, values float32
> surface dust #1 size 17.3
> surface dust #2 size 17.3
> volume #1 level 0.09852
> open "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF
> yeast fits /col_best_001.pdb" "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_002.pdb"
> "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast
> fits /col_best_003.pdb" "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_004.pdb"
> "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast
> fits /col_best_005.pdb" "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_006.pdb"
> "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast
> fits /col_best_007.pdb" "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_008.pdb"
> "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Colores/AF yeast
> fits /col_best_009.pdb" "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_010.pdb"
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_001.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_001.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_002.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_002.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_003.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_003.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_004.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_004.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_005.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_005.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_006.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_006.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_007.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_007.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13574-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_008.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_008.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13565-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_009.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_009.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13565-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Summary of feedback from opening /Users/moritz/Library/Mobile
Documents/com~apple~CloudDocs/Colores/AF yeast fits /col_best_010.pdb
---
warnings | Ignored bad PDB record found on line 2
REMARK File name col_best_010.pdb
Ignored bad PDB record found on line 3
REMARK Low-resolution fit of structure dir_001/AF-O13565-F1-model_v4.pdb into
map ../cryosparc_P49_J106_007_volume_map.mrc
Ignored bad PDB record found on line 5
REMARK Resolution anisotropy factor (Z vs. XY): 1.000000
Ignored bad PDB record found on line 6
REMARK Resolution: 6.000000 Angstrom; density cutoff: 0.176000
Ignored bad PDB record found on line 7
REMARK Angular step 15.000000 degrees, 4416 Euler angles
33 messages similar to the above omitted
Chain information for col_best_001.pdb #3
---
Chain | Description
A | No description available
Chain information for col_best_002.pdb #4
---
Chain | Description
A | No description available
Chain information for col_best_003.pdb #5
---
Chain | Description
A | No description available
Chain information for col_best_004.pdb #6
---
Chain | Description
A | No description available
Chain information for col_best_005.pdb #7
---
Chain | Description
A | No description available
Chain information for col_best_006.pdb #8
---
Chain | Description
A | No description available
Chain information for col_best_007.pdb #9
---
Chain | Description
A | No description available
Chain information for col_best_008.pdb #10
---
Chain | Description
A | No description available
Chain information for col_best_009.pdb #11
---
Chain | Description
A | No description available
Chain information for col_best_010.pdb #12
---
Chain | Description
A | No description available
> volume #1 color #b2b2b280
> volume #2 color #ffffb2c2
> hide #12 models
> hide #11 models
> hide #10 models
> hide #9 models
> hide #8 models
> hide #7 models
> hide #6 models
> hide #5 models
> hide #4 models
> show #4 models
> hide #3 models
> show #3 models
> show #5 models
> show #6 models
> show #7 models
> show #8 models
> show #9 models
> show #10 models
> show #11 models
> show #12 models
> close #3-12
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/4xhl_C_lobe_core.pdb"
Chain information for 4xhl_C_lobe_core.pdb #3
---
Chain | Description
A | No description available
> select add #3
1604 atoms, 1641 bonds, 193 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,153,0,1,0,186.69,0,0,1,264.04
> view matrix models #3,1,0,0,256.5,0,1,0,209.06,0,0,1,202.74
> ui mousemode right "rotate selected models"
> view matrix models
> #3,-0.17033,-0.24666,0.95402,318.72,-0.13446,0.96493,0.22547,216.99,-0.97617,-0.089877,-0.19752,241.3
> view matrix models
> #3,-0.1567,-0.084719,0.98401,314.33,-0.15219,0.98649,0.060697,216.37,-0.97585,-0.14025,-0.16747,242.67
> view matrix models
> #3,-0.15265,-0.027389,0.9879,312.78,-0.15884,0.9873,0.0028284,216.33,-0.97543,-0.15649,-0.15506,243.11
> view matrix models
> #3,-0.20074,-0.51202,0.83519,325.89,-0.10929,0.85893,0.5003,219.92,-0.97353,0.0091509,-0.22838,238.6
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.20074,-0.51202,0.83519,322.52,-0.10929,0.85893,0.5003,218.34,-0.97353,0.0091509,-0.22838,239.91
> view matrix models
> #3,-0.20074,-0.51202,0.83519,316.16,-0.10929,0.85893,0.5003,216.76,-0.97353,0.0091509,-0.22838,230.25
> view matrix models
> #3,-0.20074,-0.51202,0.83519,316.19,-0.10929,0.85893,0.5003,216.77,-0.97353,0.0091509,-0.22838,230.32
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.035583,-0.83093,0.55523,312.15,0.37105,0.52686,0.76469,205.26,-0.92793,0.17881,0.32707,227.12
> ui tool show "Fit in Map"
> fitmap #3 inMap #1
Fit molecule 4xhl_C_lobe_core.pdb (#3) to map
cryosparc_P49_J106_007_volume_map.mrc (#1) using 1604 atoms
average map value = 0.2343, steps = 124
shifted from previous position = 7.4
rotated from previous position = 25.9 degrees
atoms outside contour = 696, contour level = 0.098515
Position of 4xhl_C_lobe_core.pdb (#3) relative to
cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.15832689 -0.95151169 0.26373871 306.60858615
0.64353911 0.30202317 0.70330606 203.77006596
-0.74885914 0.05837392 0.66015337 218.21785171
Axis -0.32305299 0.50722044 0.79897697
Axis point 122.20713563 274.78975330 0.00000000
Rotation angle (degrees) 86.54573873
Shift along axis 178.65655861
> select subtract #3
Nothing selected
> hide #!2 models
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/4xhl_C_lobe_end.pdb"
Chain information for 4xhl_C_lobe_end.pdb #4
---
Chain | Description
A | No description available
> select add #4
449 atoms, 462 bonds, 1 pseudobond, 52 residues, 2 models selected
> view matrix models
> #4,0.94695,0.31789,-0.047162,-10.826,-0.27895,0.74018,-0.61182,25.035,-0.15958,0.59252,0.78959,-17.131
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.94695,0.31789,-0.047162,96.668,-0.27895,0.74018,-0.61182,203.05,-0.15958,0.59252,0.78959,233.31
> view matrix models
> #4,0.94695,0.31789,-0.047162,98.637,-0.27895,0.74018,-0.61182,200,-0.15958,0.59252,0.78959,236.83
> view matrix models
> #4,0.94695,0.31789,-0.047162,220.49,-0.27895,0.74018,-0.61182,212.83,-0.15958,0.59252,0.78959,151.07
> view matrix models
> #4,0.94695,0.31789,-0.047162,231.31,-0.27895,0.74018,-0.61182,216.36,-0.15958,0.59252,0.78959,163.48
> view matrix models
> #4,0.94695,0.31789,-0.047162,233.48,-0.27895,0.74018,-0.61182,217.87,-0.15958,0.59252,0.78959,168.62
> fitmap #4 inMap #1
Fit molecule 4xhl_C_lobe_end.pdb (#4) to map
cryosparc_P49_J106_007_volume_map.mrc (#1) using 449 atoms
average map value = 0.4371, steps = 208
shifted from previous position = 12
rotated from previous position = 32.1 degrees
atoms outside contour = 132, contour level = 0.098515
Position of 4xhl_C_lobe_end.pdb (#4) relative to
cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.69113669 0.59179546 -0.41485926 227.72588040
-0.72128378 0.60102393 -0.34426724 255.14537826
0.04560455 0.53716698 0.84224216 154.55474733
Axis 0.53512419 -0.27955044 -0.79717856
Axis point 446.01395496 -217.73931155 0.00000000
Rotation angle (degrees) 55.44469983
Shift along axis -72.67210643
> select subtract #4
Nothing selected
> open "/Users/moritz/Library/Mobile
> Documents/com~apple~CloudDocs/Colores/4xhl_N_lobe.pdb"
Chain information for 4xhl_N_lobe.pdb #5
---
Chain | Description
A | No description available
> select add #5
564 atoms, 575 bonds, 1 pseudobond, 69 residues, 2 models selected
> view matrix models #5,1,0,0,133.97,0,1,0,166.21,0,0,1,264.94
> view matrix models #5,1,0,0,223.03,0,1,0,203.75,0,0,1,136.68
> view matrix models #5,1,0,0,254.46,0,1,0,194.77,0,0,1,193.19
> fitmap #5 inMap #1
Fit molecule 4xhl_N_lobe.pdb (#5) to map cryosparc_P49_J106_007_volume_map.mrc
(#1) using 564 atoms
average map value = 0.3198, steps = 156
shifted from previous position = 16
rotated from previous position = 67.4 degrees
atoms outside contour = 162, contour level = 0.098515
Position of 4xhl_N_lobe.pdb (#5) relative to
cryosparc_P49_J106_007_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.40061129 0.27104603 -0.87523976 276.66835012
-0.07300854 0.96164891 0.26438821 192.97051132
0.91333474 -0.04201692 0.40503608 176.80750028
Axis -0.16589712 -0.96838901 -0.18628168
Axis point 23.31635982 0.00000000 249.77508989
Rotation angle (degrees) 67.44015931
Shift along axis -265.70500535
> select subtract #5
Nothing selected
> hide #!4 models
> hide #3 models
> open 4xhl
Summary of feedback from opening 4xhl fetched from pdb
---
note | Fetching compressed mmCIF 4xhl from http://files.rcsb.org/download/4xhl.cif
4xhl title:
Structure of S. cerevisiae Hrr25 1-394 (K38R mutant) [more info...]
Chain information for 4xhl #6
---
Chain | Description | UniProt
A | Casein kinase I homolog HRR25 | HRR25_YEAST 1-394
Non-standard residues in 4xhl #6
---
CKI — N-(2-aminoethyl)-5-chloroisoquinoline-8-sulfonamide
SO4 — sulfate ion
> color #6 #9eacdbff
> color #6 #928bdbff
> select add #6
2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 2 models selected
> view matrix models #6,1,0,0,116.76,0,1,0,162.78,0,0,1,272.63
> view matrix models #6,1,0,0,214.31,0,1,0,208.11,0,0,1,153.1
> view matrix models #6,1,0,0,245.54,0,1,0,202.68,0,0,1,194.57
> hide #!5 models
> fitmap #6 inMap #1
Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using
2811 atoms
average map value = 0.1375, steps = 100
shifted from previous position = 8.7
rotated from previous position = 12 degrees
atoms outside contour = 1628, contour level = 0.098515
Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.97987496 -0.17254456 -0.10036655 255.03434362
0.17794314 0.98289282 0.04751793 192.68596538
0.09045060 -0.06442117 0.99381517 185.88345765
Axis -0.27007944 -0.46039129 0.84563406
Axis point -929.35267507 1585.84701948 0.00000000
Rotation angle (degrees) 11.96028733
Shift along axis -0.40108880
> select subtract #6
Nothing selected
> ui tool show "Side View"
> show #!2 models
> save "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/cs_P49_J93_J106_kinase_fits.cxs"
> volume #2 level 0.06284
> volume #2 level 0.05372
> volume #2 level 0.01725
> view
> volume #1 level 0.06772
> select add #6
2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 2 models selected
> view matrix models
> #6,0.97987,-0.17254,-0.10037,255.14,0.17794,0.98289,0.047518,193.17,0.090451,-0.064421,0.99382,186.26
> fitmap #6 inMap #1
Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using
2811 atoms
average map value = 0.1375, steps = 48
shifted from previous position = 0.601
rotated from previous position = 0.119 degrees
atoms outside contour = 1545, contour level = 0.067718
Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.97995844 -0.17189236 -0.10067012 254.98725932
0.17749046 0.98287625 0.04951178 192.71670937
0.09043557 -0.06638747 0.99368713 185.97000251
Axis -0.27943973 -0.46076679 0.84238198
Axis point -924.00066790 1585.62876830 0.00000000
Rotation angle (degrees) 11.96873457
Shift along axis -3.39325106
> ui mousemode right "rotate selected models"
> view matrix models
> #6,0.88076,-0.22234,-0.41812,258.77,0.23468,0.97181,-0.022419,190.66,0.41132,-0.078381,0.90811,174.26
> fitmap #6 inMap #1
Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using
2811 atoms
average map value = 0.1432, steps = 120
shifted from previous position = 5.83
rotated from previous position = 8.71 degrees
atoms outside contour = 1544, contour level = 0.067718
Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.88312303 -0.31472882 -0.34790730 265.26051186
0.27947381 0.94856941 -0.14869585 193.78932549
0.37681310 0.03408575 0.92566195 171.24445361
Axis 0.19142788 -0.75900247 0.62231071
Axis point -270.29554587 0.00000000 847.60505810
Rotation angle (degrees) 28.51679626
Shift along axis 10.25893752
> surface dust #1 size 17.3
> surface dust #2 size 17.3
> surface dust #1 size 17.3
> surface dust #2 size 17.3
> save "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/cs_P49_J93_J106_kinase_fits.cxs"
> select subtract #6
Nothing selected
> fitmap #6 inMap #1
Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using
2811 atoms
average map value = 0.1432, steps = 96
shifted from previous position = 0.0209
rotated from previous position = 0.0335 degrees
atoms outside contour = 1545, contour level = 0.067718
Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.88318799 -0.31424338 -0.34818110 265.25060865
0.27907714 0.94873832 -0.14836292 193.78691359
0.37695482 0.03386297 0.92561243 171.26051218
Axis 0.19091373 -0.75970764 0.62160779
Axis point -270.84303671 0.00000000 847.26876748
Rotation angle (degrees) 28.50573286
Shift along axis 9.87545241
> volume #1 level 0.05186
> ui tool show "Fit in Map"
> open https://www.rbvi.ucsf.edu/chimerax/tutorials.html
Opened https://www.rbvi.ucsf.edu/chimerax/tutorials.html
> volume #1 style mesh
> fitmap #6 inMap #1
Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using
2811 atoms
average map value = 0.1432, steps = 104
shifted from previous position = 0.0173
rotated from previous position = 0.0351 degrees
atoms outside contour = 1499, contour level = 0.051864
Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.88326811 -0.31410041 -0.34810685 265.24443124
0.27916762 0.94880415 -0.14777049 193.79589028
0.37670000 0.03334080 0.92573512 171.29489506
Axis 0.18984440 -0.75975676 0.62187520
Axis point -271.66725279 0.00000000 847.80372240
Rotation angle (degrees) 28.48960246
Shift along axis 9.64147963
> volume #2 color #ffffb283
> volume #2 color #ffffb280
> volume #1 style surface
> open "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/centerTuSC_110.pdb"
Chain information for centerTuSC_110.pdb #7
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
Q | No description available
R | No description available
> hide #7 models
> open "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/TuSCmodels_new_&_old.cxs"
opened ChimeraX session
> hide #!1 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!1 models
> open "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/cs_P49_J93_J106_kinase_fits.cxs" format session
Opened cryosparc_P49_J106_007_volume_map.mrc as #1, grid size 256,256,256,
pixel 1.73, shown at level 0.0677, step 1, values float32
Opened cryosparc_P49_J93_004_volume_map.mrc as #2, grid size 256,256,256,
pixel 1.73, shown at level 0.0172, step 1, values float32
opened ChimeraX session
> volume #1 color #b2b2b258
> volume #1 color #b2b2b259
> volume #2 color #ffffb280
> ui mousemode right "map eraser"
> select add #7
2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.88312,-0.31473,-0.34791,261.83,0.27947,0.94857,-0.1487,192.81,0.37681,0.034086,0.92566,172.11,#7,1,0,0,217.03,0,1,0,216.32,0,0,1,224.26
> undo
> select subtract #6
1 model selected
> view matrix models #7,1,0,0,367.58,0,1,0,274.78,0,0,1,184.44
> view matrix models #7,1,0,0,383.13,0,1,0,271.66,0,0,1,181.34
> view matrix models #7,1,0,0,368.52,0,1,0,258.24,0,0,1,138.84
> view matrix models #7,1,0,0,373.65,0,1,0,264.87,0,0,1,135.93
Can only have one displayed volume when erasing
> view matrix models #7,1,0,0,381.89,0,1,0,263.08,0,0,1,78.051
> view matrix models #7,1,0,0,371.86,0,1,0,265.22,0,0,1,137.93
Can only have one displayed volume when erasing
> open "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/centerTuSC_110.pdb"
Chain information for centerTuSC_110.pdb #7
---
Chain | Description
A B | No description available
C | No description available
D | No description available
E | No description available
Q | No description available
R | No description available
> select add #7
38207 atoms, 38598 bonds, 2397 residues, 1 model selected
> cartoon sel
> hide (sel-residues & (protein|nucleic)) target a
> cartoon hide sel-residues
> show (sel-residues & backbone) target ab
> cartoon sel
> view matrix models #7,1,0,0,-43.187,0,1,0,-19.93,0,0,1,-76.836
> ui mousemode right "rotate selected models"
> view matrix models
> #7,0.84847,0.45734,0.26634,-197.81,-0.12109,-0.32214,0.93892,38.957,0.5152,-0.8289,-0.21795,370.39
> hide #!2 models
> hide #!1 models
> hide #!6 models
> view matrix models
> #7,-0.78452,-0.08856,-0.61375,634.28,-0.49994,-0.49523,0.7105,250.83,-0.36687,0.86424,0.34425,13.851
> view matrix models
> #7,-0.7383,-0.062768,-0.67154,634.05,-0.5342,-0.5534,0.63904,296.17,-0.41174,0.83055,0.37505,24.078
> select subtract #7
Nothing selected
> select #7/C:47
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
20 atoms, 19 bonds, 2 residues, 1 model selected
> select up
492 atoms, 494 bonds, 30 residues, 1 model selected
> color sel lime
> select clear
> select #7/Q:170
10 atoms, 10 bonds, 1 residue, 1 model selected
> select up
259 atoms, 260 bonds, 30 residues, 1 model selected
> select add #7/R:203
267 atoms, 267 bonds, 31 residues, 1 model selected
> select up
548 atoms, 550 bonds, 64 residues, 1 model selected
> color sel lime
> select #7/D
12189 atoms, 12307 bonds, 729 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dodger blue
> select clear
> select #7/E
11160 atoms, 11279 bonds, 674 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light sky blue
> select clear
> select #7/A
6909 atoms, 6984 bonds, 450 residues, 1 model selected
> select #7/B
6909 atoms, 6984 bonds, 450 residues, 1 model selected
> select #7/AB
Nothing selected
> select #7/AB
Nothing selected
> select #7/A,B
13818 atoms, 13968 bonds, 900 residues, 1 model selected
> color sel yellow
> ui tool show "Color Actions"
> color sel pale goldenrod
> color sel khaki
> color sel gold
> color sel khaki
> select clear
> show #!2 models
> select add #7
38207 atoms, 38598 bonds, 2397 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.7383,-0.062768,-0.67154,671.05,-0.5342,-0.5534,0.63904,281.76,-0.41174,0.83055,0.37505,0.68948
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.80414,-0.26184,-0.53366,693.39,-0.54215,-0.045121,0.83907,98.127,-0.24378,0.96406,-0.10567,74.723
> volume #2 level 0.4793
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.80414,-0.26184,-0.53366,682.28,-0.54215,-0.045121,0.83907,101.56,-0.24378,0.96406,-0.10567,79.555
> ui mousemode right "rotate selected models"
> view matrix models
> #7,-0.68978,-0.25355,-0.67817,695.64,-0.64875,-0.19941,0.73441,199.39,-0.32144,0.94655,-0.026945,79.427
> view matrix models
> #7,-0.68372,-0.31618,-0.65769,702.85,-0.56856,-0.33418,0.75171,205.8,-0.45746,0.88789,0.048715,105.42
> ui mousemode right "translate selected models"
> view matrix models
> #7,-0.68372,-0.31618,-0.65769,701.16,-0.56856,-0.33418,0.75171,205.13,-0.45746,0.88789,0.048715,102.48
> ui tool show "Fit in Map"
> fitmap #7 inMap #2
Fit molecule centerTuSC_110.pdb (#7) to map
cryosparc_P49_J93_004_volume_map.mrc (#2) using 38207 atoms
average map value = 0.5293, steps = 64
shifted from previous position = 3.53
rotated from previous position = 5.17 degrees
atoms outside contour = 15375, contour level = 0.47926
Position of centerTuSC_110.pdb (#7) relative to
cryosparc_P49_J93_004_volume_map.mrc (#2) coordinates:
Matrix rotation and translation
-0.72376092 -0.25058743 -0.64294328 691.96452944
-0.57765717 -0.28965214 0.76316042 192.25393123
-0.37746831 0.92374649 0.06488528 63.83963619
Axis 0.35620814 -0.58887019 -0.72549821
Axis point 380.81144853 18.20709652 0.00000000
Rotation angle (degrees) 166.97298544
Shift along axis 86.95524693
> volume #2 level 0.0172
> select clear
> show #!6 models
> select add #6
2811 atoms, 2866 bonds, 2 pseudobonds, 345 residues, 2 models selected
> fitmap #6 inMap #1
Fit molecule 4xhl (#6) to map cryosparc_P49_J106_007_volume_map.mrc (#1) using
2811 atoms
average map value = 0.1432, steps = 96
shifted from previous position = 0.0104
rotated from previous position = 0.0266 degrees
atoms outside contour = 1543, contour level = 0.067718
Position of 4xhl (#6) relative to cryosparc_P49_J106_007_volume_map.mrc (#1)
coordinates:
Matrix rotation and translation
0.88326448 -0.31429314 -0.34794206 265.25037566
0.27909242 0.94871554 -0.14847978 193.79339019
0.37676422 0.03403892 0.92568357 171.24941094
Axis 0.19126658 -0.75944048 0.62182574
Axis point -270.74685697 0.00000000 847.65443656
Rotation angle (degrees) 28.49823674
Shift along axis 10.04627679
> select clear
> save "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/cs_P49_J93_J106_kinase_fits.cxs"
> ui mousemode right "map eraser"
> hide #!1 models
> select add #8
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,363.71,0,1,0,217.51,0,0,1,220.3
> view matrix models #8,1,0,0,371.59,0,1,0,205.49,0,0,1,218.22
> volume erase #2 center 371.59,205.49,218.22 radius 40.302
Opened cryosparc_P49_J93_004_volume_map.mrc copy as #9, grid size 256,256,256,
pixel 1.73, shown at step 1, values float32
> surface dust #9 size 17.3
> view matrix models #8,1,0,0,370.19,0,1,0,205.79,0,0,1,214.36
> view matrix models #8,1,0,0,392.95,0,1,0,147.21,0,0,1,231.4
> view matrix models #8,1,0,0,373.51,0,1,0,136.99,0,0,1,231.23
> view matrix models #8,1,0,0,359.25,0,1,0,134.43,0,0,1,230.66
> view matrix models #8,1,0,0,372.13,0,1,0,132.68,0,0,1,234.35
> view matrix models #8,1,0,0,373.37,0,1,0,131.75,0,0,1,231.07
> view matrix models #8,1,0,0,374.44,0,1,0,133.85,0,0,1,231.35
> volume erase #9 center 374.44,133.85,231.35 radius 75.29
> view matrix models #8,1,0,0,385.19,0,1,0,280.65,0,0,1,100.54
> view matrix models #8,1,0,0,369.08,0,1,0,289,0,0,1,126.87
> view matrix models #8,1,0,0,386.31,0,1,0,316.5,0,0,1,111.88
> view matrix models #8,1,0,0,325.52,0,1,0,365.28,0,0,1,141.79
> volume erase #9 center 325.52,365.28,141.79 radius 75.29
> view matrix models #8,1,0,0,249.96,0,1,0,319.39,0,0,1,71.606
> view matrix models #8,1,0,0,326.31,0,1,0,225.05,0,0,1,86.547
> view matrix models #8,1,0,0,351.22,0,1,0,206.49,0,0,1,125.15
> view matrix models #8,1,0,0,313.56,0,1,0,162.42,0,0,1,66.373
> view matrix models #8,1,0,0,406.96,0,1,0,194.11,0,0,1,70.874
> view matrix models #8,1,0,0,398.4,0,1,0,240.91,0,0,1,116.42
> volume erase #9 center 398.4,240.91,116.42 radius 75.29
> view matrix models #8,1,0,0,372.27,0,1,0,351.16,0,0,1,35.303
> ui mousemode right "map eraser"
> select add #8
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #8,1,0,0,306.08,0,1,0,349.2,0,0,1,211.87
> view matrix models #8,1,0,0,295.86,0,1,0,377.11,0,0,1,205.67
> view matrix models #8,1,0,0,297.89,0,1,0,378.44,0,0,1,210.3
> volume erase #2 center 297.89,378.44,210.3 radius 68.757
Opened cryosparc_P49_J93_004_volume_map.mrc copy as #10, grid size
256,256,256, pixel 1.73, shown at step 1, values float32
> surface dust #10 size 17.3
> view matrix models #8,1,0,0,281.35,0,1,0,363.72,0,0,1,178.33
> view matrix models #8,1,0,0,237.54,0,1,0,398.02,0,0,1,193.89
> volume erase #10 center 237.54,398.02,193.89 radius 68.646
> view matrix models #8,1,0,0,249.43,0,1,0,414.16,0,0,1,164.72
> volume erase #10 center 249.43,414.16,164.72 radius 68.646
> view matrix models #8,1,0,0,301.26,0,1,0,358.72,0,0,1,95.652
> view matrix models #8,1,0,0,291.96,0,1,0,269.15,0,0,1,72.692
> volume erase #10 center 291.96,269.15,72.692 radius 68.646
> view matrix models #8,1,0,0,298.7,0,1,0,353.65,0,0,1,100.52
> volume erase #10 center 298.7,353.65,100.52 radius 68.646
> view matrix models #8,1,0,0,209.77,0,1,0,341.8,0,0,1,107.53
> volume erase #10 center 209.77,341.8,107.53 radius 68.646
> view matrix models #8,1,0,0,225.86,0,1,0,274.62,0,0,1,38.108
> volume erase #10 center 225.86,274.62,38.108 radius 68.646
> view matrix models #8,1,0,0,229.32,0,1,0,238.59,0,0,1,27.323
> view matrix models #8,1,0,0,341.4,0,1,0,342.4,0,0,1,118.74
> volume erase #10 center 341.4,342.4,118.74 radius 68.646
> view matrix models #8,1,0,0,389.63,0,1,0,278.17,0,0,1,147.8
> volume erase #10 center 389.63,278.17,147.8 radius 68.646
> view matrix models #8,1,0,0,373.84,0,1,0,165.4,0,0,1,199.95
> volume erase #10 center 373.84,165.4,199.95 radius 68.646
> view matrix models #8,1,0,0,387.14,0,1,0,169.4,0,0,1,242.25
> view matrix models #8,1,0,0,411.91,0,1,0,247.77,0,0,1,280.33
> volume erase #10 center 411.91,247.77,280.33 radius 68.646
> view matrix models #8,1,0,0,364.19,0,1,0,100.95,0,0,1,209.21
> volume erase #10 center 364.19,100.95,209.21 radius 68.646
> view matrix models #8,1,0,0,223.34,0,1,0,50.114,0,0,1,2.1595
> view matrix models #8,1,0,0,253.04,0,1,0,72.112,0,0,1,40.565
> view matrix models #8,1,0,0,232.15,0,1,0,183.15,0,0,1,61.671
> view matrix models #8,1,0,0,235.43,0,1,0,182.39,0,0,1,51.39
> volume erase #10 center 235.43,182.39,51.39 radius 68.646
> view matrix models #8,1,0,0,195.65,0,1,0,232.08,0,0,1,39.419
> view matrix models #8,1,0,0,144.97,0,1,0,223.78,0,0,1,-14.378
> view matrix models #8,1,0,0,74.122,0,1,0,200.05,0,0,1,49.758
> volume erase #10 center 74.122,200.05,49.758 radius 68.646
> view matrix models #8,1,0,0,100.62,0,1,0,204.65,0,0,1,37.983
> view matrix models #8,1,0,0,115.35,0,1,0,214.35,0,0,1,39.987
> volume erase #10 center 115.35,214.35,39.987 radius 68.646
> view matrix models #8,1,0,0,168.54,0,1,0,30.519,0,0,1,84.812
> view matrix models #8,1,0,0,291.9,0,1,0,59.451,0,0,1,123.68
> view matrix models #8,1,0,0,293.43,0,1,0,83.011,0,0,1,92.626
> volume erase #10 center 293.43,83.011,92.626 radius 68.646
> view matrix models #8,1,0,0,374.23,0,1,0,80.14,0,0,1,208.56
> toolshed show
Downloading bundle ChimeraX_PhenixUI-1.3.7-py3-none-any.whl
Installed ChimeraX-PhenixUI (1.3.7)
> ui tool show "Local EM Fitting"
> save "/Users/moritz/Library/Mobile Documents/com~apple~CloudDocs/Chimera
> sessions/cs_P49_J93_J106_kinase_fits.cxs"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> volume step 1
Error running startup command 'volume step 1': No volumes specified
UCSF ChimeraX version: 1.8 (2024-06-10)
© 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 560 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: iMac
Model Identifier: iMac18,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
System Firmware Version: 529.140.2.0.0
OS Loader Version: 577.140.2~22
SMC Version (system): 2.40f1
Software:
System Software Overview:
System Version: macOS 13.6.9 (22G830)
Kernel Version: Darwin 22.6.0
Time since boot: 81 days, 18 hours, 25 minutes
Graphics/Displays:
Radeon Pro 560:
Chipset Model: Radeon Pro 560
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67ef
Revision ID: 0x00c0
ROM Revision: 113-C980AA-921
VBIOS Version: 113-C9810A1X-017
EFI Driver Version: 01.00.921
Metal Support: Metal 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: 4096 x 2304 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.16
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: 1.6.4
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: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
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: 1.8
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: 1.5.17
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: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
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: 3.0.47
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: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
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 (8)
comment:1 by , 12 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 , 12 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
comment:4 by , 12 months ago
Thanks Michelle. That is interesting that this crash can happen with only the built-in iMac display. The crash traceback says something about the display changed
[NSApplication(ScreenHandling) _reactToDisplayChanges:]
Do you recall if you changed the screen resolution, or maybe put ChimeraX in full-screen mode, or maybe use multiple desktops? I'm hoping to find out what triggers this crash. I've spent dozens of hours trying to make it crash with my machine in the last several months and have failed so far. But 100 people have reported this Mac ChimeraX crash so it must be easy if you know the secret step.
comment:5 by , 12 months ago
One more clue is that the crash report says ChimeraX was in the background -- in other words it wasn't the active application when it crashed.
One more question -- did your iMac sleep and then ChimeraX crash when it woke up?
comment:6 by , 12 months ago
Sorry for pestering you so much about this crash. I have a meeting today to discuss how we are going to handle it for the upcoming ChimeraX 1.9 release.
I noticed in the crash report you try to set the "volume step 1" when ChimeraX starts, but that only works on volumes that are already opened. Here's the magic command to make sure your volumes always open and display step 1
volume defaultvalues limitVoxelCount false saveSettings true
If you use this command one time it will remember the setting and never use step 2 when opening volumes in this or future ChimeraX sessions.
comment:7 by , 12 months ago
Thanks for the tip on the volume step setting. I will try that.
And yes, I had ChimeraX running in the background and my computer had been sleeping. I was not actually using it when it crashed. Could it be related to my poor internet connection? I often have connectivity problems on my desktop computer here in the lab—it tends to lose connection, especially when I haven’t been using it over night.
comment:8 by , 12 months ago
I don't think the crash is caused by any problem on your computer such as internet connection. It is just a bug in the Qt window toolkit. Sometimes just waking from sleep crashes ChimeraX on Mac in the newer Qt versions we are using. Thanks for all the info you have provided. I was never sure that just waking from sleep could cause this crash with no second monitor.
Note:
See TracTickets
for help on using tickets.
Did you have a second display connected to your iMac when ChimeraX crashed?
The ChimeraX crash was in the Qt window toolkit ChimeraX uses. We've seen this reported many times when an external display is unplugged or plugged in. But I'm wondering if the same crash can happen without changing a display connection.
The ChimeraX 1.9 release candidate and daily builds are using a newer Qt version (6.7 instead of 6.6) and this seems to crash less often, but we've still seen the same crash in Qt 6.7.