![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 12 months ago
Closed 12 months ago
#16146 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-14.4.1-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 0x00007ff8525ad100 (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.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, psutil._psutil_osx, psutil._psutil_posix, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 118)
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{
"uptime" : 270000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 132670576,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 1367,
"osVersion" : {
"train" : "macOS 14.4.1",
"build" : "23E224",
"releaseType" : "User"
},
"captureTime" : "2024-10-19 18:34:49.9737 +0100",
"codeSigningMonitor" : 0,
"incident" : "C1E53B64-B3C8-499F-8204-68785D2FBC9F",
"pid" : 53131,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-10-19 17:41:12.4102 +0100",
"procStartAbsTime" : 275063401653802,
"procExitAbsTime" : 278280967991956,
"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":"15729EDA-50B5-5474-9D20-8B1DA717CAA6","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "80D9B92F-7DBD-7C33-824E-8D92D240C367",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 5442,
"bridgeVersion" : {"build":"21P4222","train":"8.4"},
"sleepWakeUUID" : "2DED4EEE-ECE4-48E2-8B90-77896A02B0E2",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4320600064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 101872000-101876000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/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":53131},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4320600064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 101872000-101876000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/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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"vmSummary" : "ReadOnly portion of Libraries: Total=1.4G resident=0K(0%) swapped_out_or_unallocated=1.4G(100%)\nWritable regions: Total=2.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG image 948K 72 \nCG raster data 8K 1 \nColorSync 256K 31 \nCoreAnimation 1564K 204 \nCoreGraphics 24K 4 \nCoreUI image data 5936K 64 \nFoundation 48K 2 \nIOKit 23.3M 3 \nImage IO 100K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.6G 869 \nMALLOC guard page 64K 16 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 24K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 224K 56 \nStack 186.4M 58 \nStack Guard 56.0M 1 \nVM_ALLOCATE 389.8M 569 \nVM_ALLOCATE (reserved) 352.0M 4 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 48.6M 895 \n__DATA_CONST 66.0M 472 \n__DATA_DIRTY 1850K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 225.8M 244 \n__OBJC_RO 71.7M 1 \n__OBJC_RW 2196K 2 \n__TEXT 1.1G 895 \ndyld private memory 648K 8 \nmapped file 576.1M 111 \nshared memory 3528K 33 \n=========== ======= ======= \nTOTAL 4.7G 4866 \nTOTAL, minus reserved VM space 4.4G 4866 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "0d55d7cc7e1201a304b3671cd1b34d5984140fec",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "654439cdafbf5b61207873a9",
"factorPackIds" : {
},
"deploymentId" : 240000004
},
{
"rolloutId" : "6434420a89ec2e0a7a38bf5a",
"factorPackIds" : {
},
"deploymentId" : 240000011
}
],
"experiments" : [
{
"treatmentId" : "c47ab4cc-c9c3-4b5d-a87c-e2433ce02597",
"experimentId" : "6639bc6ba73d460582162323",
"deploymentId" : 400000006
},
{
"treatmentId" : "45f4e2a5-551b-4bc2-a2dc-19c244dda8f8",
"experimentId" : "6643969b3099cf28e049862f",
"deploymentId" : 400000007
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
> ui tool hide "command line interface"
> ui tool show clix
Error running startup command 'ui tool show clix': No running or installed
tool named "clix"
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/jk658/Desktop/ap3_coot4.pdb
Summary of feedback from opening /Users/jk658/Desktop/ap3_coot4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA D 2 ILE D 10 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP D 11 MET D 13 1
3
CONECT record to nonexistent atom: (47, 52)
CONECT record to nonexistent atom: (49, 50)
CONECT record to nonexistent atom: (49, 51)
Start residue of secondary structure not found: HELIX 1 1 ALA D 2 ILE D 10 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP D 11 MET D 13 1
3
Start residue of secondary structure not found: HELIX 3 3 LEU D 18 ASN D 27 1
10
Start residue of secondary structure not found: HELIX 4 4 GLU D 32 GLN D 45 1
14
Start residue of secondary structure not found: HELIX 5 5 GLU D 46 LYS D 48 1
3
435 messages similar to the above omitted
Chain information for ap3_coot4.pdb
---
Chain | Description
1.1/A | No description available
1.1/B | No description available
1.2/B | No description available
1.1/C | No description available
1.1/D | No description available
1.1/E | No description available
1.1/F | No description available
1.3/F | No description available
1.1/G 1.1/H | No description available
> open /Users/jk658/Desktop/ap3_coot4.pdb
Summary of feedback from opening /Users/jk658/Desktop/ap3_coot4.pdb
---
warnings | Start residue of secondary structure not found: HELIX 1 1 ALA D 2 ILE D 10 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP D 11 MET D 13 1
3
Start residue of secondary structure not found: HELIX 1 1 ALA D 2 ILE D 10 1 9
Start residue of secondary structure not found: HELIX 2 2 ASP D 11 MET D 13 1
3
Start residue of secondary structure not found: HELIX 3 3 LEU D 18 ASN D 27 1
10
437 messages similar to the above omitted
Chain information for ap3_coot4.pdb
---
Chain | Description
2.1/A | No description available
2.1/B | No description available
2.2/B | No description available
2.1/C | No description available
2.1/D | No description available
2.1/E | No description available
2.1/F | No description available
2.3/F | No description available
2.1/G 2.1/H | No description available
> show cartoons
> hide atoms
> toolshed show
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
Downloading bundle ChimeraX_clix-0.1.9-py3-none-any.whl
Installed ChimeraX-clix (0.1.9)
> ui tool show CliX
> open /Users/jk658/Desktop/AP3_tube_5_class1_filtsharp.mrc
Opened AP3_tube_5_class1_filtsharp.mrc as #3, grid size 150,150,150, pixel
2.4, shown at level 0.00229, step 1, values float32
> volume #3 level 0.003775
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 37958 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
~worm
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> hide #!3 models
> ui tool show Matchmaker
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #2.1/F to #1.1/E pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ap3_coot4.pdb, chain E (#1.1) with ap3_coot4.pdb, chain F (#2.1),
sequence alignment score = 874.1
RMSD between 168 pruned atom pairs is 0.080 angstroms; (across all 168 pairs:
0.080)
> open /Users/jk658/Desktop/AP3_tube_5_class1_filtsharp.mrc
Opened AP3_tube_5_class1_filtsharp.mrc as #4, grid size 150,150,150, pixel
2.4, shown at level 0.00229, step 1, values float32
> molmap #2 2
Opened map 2 as #5, grid size 193,266,197, pixel 0.667, shown at level 0.186,
step 1, values float32
> select #4
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.99891,-0.0076402,0.045991,-5.9477,0.0071529,0.99992,0.01075,-3.0289,-0.046069,-0.010409,0.99888,10.342
> view matrix models
> #4,-0.98202,0.1875,-0.021917,326.61,-0.18793,-0.96009,0.20713,351.94,0.017794,0.20753,0.97807,-36.883
> view matrix models
> #4,-0.99377,0.098547,0.052119,332.6,-0.082341,-0.96402,0.25276,326.18,0.075153,0.2469,0.96612,-52.323
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99377,0.098547,0.052119,326.69,-0.082341,-0.96402,0.25276,325.76,0.075153,0.2469,0.96612,-53.244
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.99294,0.060495,0.10204,325.22,-0.051931,-0.99506,0.084599,353.34,0.10665,0.078703,0.99118,-32.805
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.99294,0.060495,0.10204,323.18,-0.051931,-0.99506,0.084599,354.82,0.10665,0.078703,0.99118,-34.26
> ui tool show "Fit in Map"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> fitmap #4 inMap #5
Fit map AP3_tube_5_class1_filtsharp.mrc in map map 2 using 33640 points
correlation = 0.4486, correlation about mean = 0.3272, overlap = 34.25
steps = 148, shift = 6.42, angle = 5.59 degrees
Position of AP3_tube_5_class1_filtsharp.mrc (#4) relative to map 2 (#5)
coordinates:
Matrix rotation and translation
0.99993132 -0.01169637 0.00074589 2.01868940
0.01169633 0.99993160 0.00006322 -2.37018635
-0.00074658 -0.00005450 0.99999972 -0.40622599
Axis -0.00502202 0.06367010 0.99795836
Axis point 200.56119996 171.17010959 0.00000000
Rotation angle (degrees) 0.67153796
Shift along axis -0.56644453
> volume #4 color #b2b2b2
> close #5
> select clear
> color /a #4e7767ff
> color /b #ea394cff
> color /c #b2b2b2ff
> color /d #50b1beff
> color /e /f /g /h yellow
> set bgColor white
> lighting full
> lighting shadows false
> graphics silhouettes true
> volume #4 color #b2b2b21a
> volume #3 color #b2b2b21a
> select clear
> ui tool show Matchmaker
> matchmaker #2.1/G to #1.1/H pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ap3_coot4.pdb, chain H (#1.1) with ap3_coot4.pdb, chain G (#2.1),
sequence alignment score = 849.2
RMSD between 163 pruned atom pairs is 0.001 angstroms; (across all 163 pairs:
0.001)
> undo
> matchmaker #2.1/H to #1.1/G pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ap3_coot4.pdb, chain G (#1.1) with ap3_coot4.pdb, chain H (#2.1),
sequence alignment score = 849.2
RMSD between 163 pruned atom pairs is 0.001 angstroms; (across all 163 pairs:
0.001)
> volume #4 level 0.002661
> volume #4 level 0.003151
> volume #4 level 0.004742
> molmap #2 2
Opened map 2 as #5, grid size 191,266,197, pixel 0.667, shown at level 0.187,
step 1, values float32
> close #5
> volume #4 level 0.006151
> volume #3 level 0.004877
Drag select of 3 residues
> select clear
> select #1.1/D:123
7 atoms, 7 bonds, 1 residue, 1 model selected
> select add #2.1/A:127
14 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> select clear
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> show #!2.1 models
> hide #!2.1 models
> select add #1.3/F:210
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 7 residues, 1 model selected
> color sel orange
> select clear
> select #1.3/F:211
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
53 atoms, 54 bonds, 7 residues, 1 model selected
> hide sel cartoons
Drag select of 2 residues
> select up
106 atoms, 108 bonds, 14 residues, 2 models selected
> hide sel cartoons
> select clear
> select add #1.1/D:157
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select add #1.1/D:158
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #1.1/D:187
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> select clear
> color #1.2-3#2.2-3#!1.1 byhetero
> volume #3 level 0.003959
> select #1.1/G:130
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
70 atoms, 70 bonds, 9 residues, 1 model selected
> select up
1312 atoms, 1335 bonds, 163 residues, 1 model selected
> color sel magenta
> select clear
> hide #!1 models
> select add #2
19081 atoms, 19415 bonds, 1 pseudobond, 2395 residues, 5 models selected
> show sel & #2.2-3 cartoons
> hide sel & #2.2-3 cartoons
> select clear
> hide #!2 models
> show #!2 models
> select add #2
19081 atoms, 19415 bonds, 1 pseudobond, 2395 residues, 5 models selected
> show sel & #2.2-3 cartoons
> select clear
Drag select of 7 residues
> hide sel cartoons
> select add #2.3
53 atoms, 54 bonds, 7 residues, 1 model selected
> select subtract #2.3
Nothing selected
> show #!2.1 models
> select add #2.1/A:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select add #2.1/A:194
18 atoms, 16 bonds, 2 residues, 1 model selected
> show sel atoms
> select add #2.1/A:162
26 atoms, 23 bonds, 3 residues, 1 model selected
> show sel atoms
> color sel byhetero
> select clear
> molmap #2 2
Opened map 2 as #5, grid size 191,266,197, pixel 0.667, shown at level 0.187,
step 1, values float32
> fitmap #4 inMap #5
Fit map AP3_tube_5_class1_filtsharp.mrc in map map 2 using 4939 points
correlation = 0.5513, correlation about mean = 0.04235, overlap = 19.6
steps = 148, shift = 5.84, angle = 4.87 degrees
Position of AP3_tube_5_class1_filtsharp.mrc (#4) relative to map 2 (#5)
coordinates:
Matrix rotation and translation
0.99995752 -0.00165526 -0.00906825 2.43244853
0.00155179 0.99993375 -0.01140591 1.65515043
0.00908653 0.01139135 0.99989383 -3.43938927
Axis 0.77756269 -0.61921816 0.10938524
Axis point 0.00000000 308.22143295 169.93907506
Rotation angle (degrees) 0.83995398
Shift along axis 0.49026361
> close #5
> volume #4 level 0.004534
> hide #!1.1 models
> show #!1.1 models
> hide #!1.1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1.1 models
> hide #!1.1 models
> select clear
> select #2.1/H:129
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
70 atoms, 70 bonds, 9 residues, 1 model selected
> select up
1312 atoms, 1335 bonds, 163 residues, 1 model selected
> color sel magenta
> select clear
> volume #4 level 0.004599
> ui tool show Rotamers
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> select #2.1/A:125
9 atoms, 8 bonds, 1 residue, 1 model selected
> swapaa interactive sel LYS rotLib Dunbrack
ap3_coot4.pdb #2.1/A LYS 125: phi -103.1, psi 6.2 trans
Changed 438 bond radii
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> swapaa interactive sel LYS rotLib Dunbrack
ap3_coot4.pdb #!2.1/A LYS 125: phi -103.1, psi 6.2 trans
Changed 438 bond radii
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> swapaa #!2.1/A:125 LYS criteria 9 rotLib Dunbrack retain false
Using Dunbrack library
ap3_coot4.pdb #!2.1/A LYS 125: phi -103.1, psi 6.2 trans
Applying LYS rotamer (chi angles: -61.8 -64.7 -71.6 -176.1) to ap3_coot4.pdb
#!2.1/A LYS 125
> select clear
> ui tool show "Side View"
> lighting full
> lighting shadows false
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
> ui tool hide "command line interface"
> ui tool show clix
> show atoms
> style stick
Changed 0 atom styles
> hide atoms
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-5.5.17
OpenGL renderer: AMD Radeon Pro 5500M 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: MacBookPro16,1
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.4222.0.0,0)
OS Loader Version: 580~1678
Software:
System Software Overview:
System Version: macOS 14.4.1 (23E224)
Kernel Version: Darwin 23.4.0
Time since boot: 10 days, 3 hours, 12 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: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5500M:
Chipset Model: AMD Radeon Pro 5500M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0040
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32206U1-020
Option ROM Version: 113-D32206U1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
Connection Type: Internal
DELL P2719H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: HLSNQS2
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.59
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-Clipper: 0.23.1
ChimeraX-clix: 0.1.9
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-ISOLDE: 1.8
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-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 (2)
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 |
This ChimeraX crash is caused by a bug in the Qt 6.6 window toolkit and usually occurs when unplugging or plugging in an external display or waking from sleep. We believe the crash does not happen in Qt 6.7 which is used by the ChimeraX daily build. So use the daily build if you want to avoid this, or avoid changing external displays or sleeping while ChimeraX is running.
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Reported by Jonathan