id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
17878	Crash on Mac waking from sleep	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-15.5-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 0x0000000201286200 (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, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.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.spatial._ckdtree, scipy._lib.messagestream, 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, markupsafe._speedups, 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.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets (total: 100)


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    ""path"" : ""\/System\/Library\/PrivateFrameworks\/WindowManagement.framework\/Versions\/A\/WindowManagement"",
    ""name"" : ""WindowManagement"",
    ""CFBundleVersion"" : ""278.4.7""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703287062528,
    ""CFBundleShortVersionString"" : ""6.9"",
    ""CFBundleIdentifier"" : ""com.apple.Foundation"",
    ""size"" : 14620850,
    ""uuid"" : ""3e72de1d-c81a-3c8b-9c06-5b1e3186de47"",
    ""path"" : ""\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation"",
    ""name"" : ""Foundation"",
    ""CFBundleVersion"" : ""3502.1.401""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140703265808384,
    ""size"" : 289750,
    ""uuid"" : ""c320442e-e6e3-321d-a051-692d7ed82dfa"",
    ""path"" : ""\/usr\/lib\/system\/libxpc.dylib"",
    ""name"" : ""libxpc.dylib""
  },
  {
    ""source"" : ""P"",
    ""arch"" : ""x86_64"",
    ""base"" : 140707591634944,
    ""CFBundleShortVersionString"" : ""1.0"",
    ""CFBundleIdentifier"" : ""com.apple.MediaServices"",
    ""size"" : 527935,
    ""uuid"" : ""4228eee0-6ccf-36cc-a6bb-46d493c69ecc"",
    ""path"" : ""\/System\/Library\/PrivateFrameworks\/MediaServices.framework\/Versions\/A\/MediaServices"",
    ""name"" : ""MediaServices"",
    ""CFBundleVersion"" : ""4024.500.30""
  }
],
  ""sharedCache"" : {
  ""base"" : 140703236718592,
  ""size"" : 25769803776,
  ""uuid"" : ""6e28f2b9-5b29-30c6-af7c-47d23bf9ec34""
},
  ""legacyInfo"" : {
  ""threadTriggered"" : {
    ""name"" : ""CrBrowserMain"",
    ""queue"" : ""com.apple.main-thread""
  }
},
  ""logWritingSignature"" : ""14128c823c5f722cf860af03e8db617a8ce0b14c"",
  ""trialInfo"" : {
  ""rollouts"" : [
    {
      ""rolloutId"" : ""6297d96be2c9387df974efa4"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000032
    },
    {
      ""rolloutId"" : ""67181b10c68c361a728c7cfa"",
      ""factorPackIds"" : {

      },
      ""deploymentId"" : 240000005
    }
  ],
  ""experiments"" : [
    {
      ""treatmentId"" : ""4cfb9672-7b7b-42d8-a7dc-b675ffa2f5dc"",
      ""experimentId"" : ""67f46877b1ea9f1f114b8d0b"",
      ""deploymentId"" : 400000001
    },
    {
      ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"",
      ""experimentId"" : ""6685b283afc7c17197d69eec"",
      ""deploymentId"" : 400000012
    }
  ]
},
  ""reportNotes"" : [
  ""RIP register does not match crashing frame (0x0 vs 0x7FF895B12AE0)""
]
}
===== Log before crash start =====
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/bs18klrh/Downloads/cryosparc_P216_J41_013_volume_map_sharp.mrc

Opened cryosparc_P216_J41_013_volume_map_sharp.mrc as #1, grid size
448,448,448, pixel 0.74, shown at level 0.0751, step 2, values float32  

> volume #1 step 1

> volume #1 level 0.1377

> open ""/Users/bs18klrh/Desktop/BTD_nano/Reprocessed correct pixel
> size/BTDNano_Map_1.mrc""

Opened BTDNano_Map_1.mrc as #2, grid size 512,512,512, pixel 0.74, shown at
level 0.0772, step 2, values float32  

> open ""/Users/bs18klrh/Desktop/BTD_nano/Reprocessed correct pixel
> size/BTDNano_Model_1_CaBLAM1.03.pdb""

Summary of feedback from opening /Users/bs18klrh/Desktop/BTD_nano/Reprocessed
correct pixel size/BTDNano_Model_1_CaBLAM1.03.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
16624 messages similar to the above omitted  
  
Chain information for BTDNano_Model_1_CaBLAM1.03.pdb #3  
---  
Chain | Description  
A B C D | No description available  
  

> select add #1

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.034506,-0.99233,-0.11873,354.64,-0.99844,0.029023,0.047601,318.97,-0.043789,0.12019,-0.99178,300.55

> ui mousemode right ""translate selected models""

> view matrix models
> #1,-0.034506,-0.99233,-0.11873,355.53,-0.99844,0.029023,0.047601,318.72,-0.043789,0.12019,-0.99178,350.77

> view matrix models
> #1,-0.034506,-0.99233,-0.11873,381.55,-0.99844,0.029023,0.047601,348.69,-0.043789,0.12019,-0.99178,356.24

> view matrix models
> #1,-0.034506,-0.99233,-0.11873,382.8,-0.99844,0.029023,0.047601,345.29,-0.043789,0.12019,-0.99178,354.16

> view matrix models
> #1,-0.034506,-0.99233,-0.11873,381.66,-0.99844,0.029023,0.047601,340.04,-0.043789,0.12019,-0.99178,354.15

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,-0.049104,-0.99036,-0.12952,385.45,-0.99871,0.047021,0.019088,341.59,-0.012814,0.13029,-0.99139,347.28

> view matrix models
> #1,0.86219,-0.50033,-0.079368,145.28,-0.50619,-0.85707,-0.095976,427.9,-0.020004,0.12292,-0.99221,349.82

> view matrix models
> #1,0.74049,-0.66486,-0.098118,195.67,-0.67178,-0.73646,-0.079591,432.78,-0.019343,0.12485,-0.99199,349.36

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.74049,-0.66486,-0.098118,193.97,-0.67178,-0.73646,-0.079591,438.24,-0.019343,0.12485,-0.99199,349.39

> volume #2 step 1

> volume #2 level 0.2006

> view matrix models
> #1,0.74049,-0.66486,-0.098118,195.97,-0.67178,-0.73646,-0.079591,437.8,-0.019343,0.12485,-0.99199,349.05

> ui mousemode right ""rotate selected models""

> view matrix models
> #1,0.63496,-0.76675,-0.094446,229.78,-0.77254,-0.63068,-0.073625,436.03,-0.0031129,0.11971,-0.9928,347.34

> view matrix models
> #1,0.71883,-0.69215,-0.064974,198.88,-0.695,-0.71766,-0.04407,432.95,-0.016126,0.076836,-0.99691,357.26

> ui mousemode right ""translate selected models""

> view matrix models
> #1,0.71883,-0.69215,-0.064974,199.54,-0.695,-0.71766,-0.04407,432.61,-0.016126,0.076836,-0.99691,358.26

> view matrix models
> #1,0.71883,-0.69215,-0.064974,194.36,-0.695,-0.71766,-0.04407,428.34,-0.016126,0.076836,-0.99691,357.8

> view matrix models
> #1,0.71883,-0.69215,-0.064974,197.24,-0.695,-0.71766,-0.04407,430.58,-0.016126,0.076836,-0.99691,358.04

> ui tool show ""Fit in Map""

> fitmap #1 inMap #2

Fit map cryosparc_P216_J41_013_volume_map_sharp.mrc in map BTDNano_Map_1.mrc
using 328048 points  
correlation = 0.9582, correlation about mean = 0.8501, overlap = 3.798e+04  
steps = 136, shift = 1.22, angle = 7.39 degrees  
  
Position of cryosparc_P216_J41_013_volume_map_sharp.mrc (#1) relative to
BTDNano_Map_1.mrc (#2) coordinates:  
Matrix rotation and translation  
0.64472097 -0.76441799 0.00004202 209.27333899  
-0.76441799 -0.64472097 -0.00000041 423.01853679  
0.00002740 -0.00003186 -1.00000000 368.87866670  
Axis -0.90683113 0.42149412 -0.00001183  
Axis point 0.00000000 260.14604205 184.43592284  
Rotation angle (degrees) 179.99900632  
Shift along axis -11.48011537  
  

> volume #1 level 0.1885

> select subtract #1

Nothing selected  

> volume #2 level 0.23

> volume #1 level 0.2103

> hide #!3 models

> volume #2 level 0.1875

> volume #1 level 0.1921

> ui tool show ""Hide Dust""

> surface dust #1 size 4.44

> surface dust #2 size 4.44

> lighting soft

> volume #1 level 0.1776

> hide #!2 models

> show #!2 models

> hide #!1 models

> show #!1 models

> hide #!2 models

> show #!2 models

> show #!3 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!3 models

> show #!2 models

> show #!3 models

> hide #!2 models

> hide #!1 models

> hide #!3 models

> show #!2 models

> show #!1 models

> volume subtract #1 #2

Opened volume difference as #4, grid size 448,448,448, pixel 0.74, shown at
step 1, values float32  

> volume #4 level 0.2622

> show #!3 models

> volume subtract #2 #1

Opened volume difference as #5, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32  

> close #4

> volume #5 level 0.257

> volume #5 level 0.2053

> show atoms

> ui tool show ""Side View""

> set bgColor white

> hide atoms

> volume #5 level 0.1732

> surface dust #5 size 4.44

> show #!1 models

> hide #!1 models

> save ""/Users/bs18klrh/OneDrive - University of
> Leeds/Research_Postgrad/Thesis
> Bits/Nanodiscs/BTD_Amph_Nano_volumesubtractsession.cxs""

> close

> open ""/Users/bs18klrh/Library/CloudStorage/OneDrive-
> UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323 AM237/Final(_)
> July'24/TRPC5_AM237_allribbons_all_lig_2lip_refined_024.pdb""

Summary of feedback from opening
/Users/bs18klrh/Library/CloudStorage/OneDrive-
UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323 AM237/Final(_)
July'24/TRPC5_AM237_allribbons_all_lig_2lip_refined_024.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
16930 messages similar to the above omitted  
  
Chain information for TRPC5_AM237_allribbons_all_lig_2lip_refined_024.pdb #1  
---  
Chain | Description  
A B C D | No description available  
  

> open ""/Users/bs18klrh/Library/CloudStorage/OneDrive-
> UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323 AM237/Final(_)
> July'24/J155_ResolveMap.mrc""

Opened J155_ResolveMap.mrc as #2, grid size 143,143,172, pixel 0.74,0.74,0.74,
shown at level 4.55, step 1, values float32  

> open ""/Users/bs18klrh/Downloads/cryosparc_P18_J28_011_volume_map_sharp
> (2).mrc""

Opened cryosparc_P18_J28_011_volume_map_sharp (2).mrc as #3, grid size
512,512,512, pixel 0.74, shown at level 0.0686, step 2, values float32  

> volume #2 level 1.308

> volume #3 step 1

> volume #3 level 0.1326

> select add #3

2 models selected  

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.9686,0.23082,-0.092334,347.21,0.21322,0.9623,0.16887,-66.171,0.12783,0.14388,-0.9813,334.78

> view matrix models
> #3,-0.97023,0.21441,-0.11261,354.58,0.209,0.9762,0.057974,-46.386,0.12236,0.032713,-0.99195,358.95

> ui mousemode right ""translate selected models""

> view matrix models
> #3,-0.97023,0.21441,-0.11261,340.65,0.209,0.9762,0.057974,-76.42,0.12236,0.032713,-0.99195,305.98

> view matrix models
> #3,-0.97023,0.21441,-0.11261,332.59,0.209,0.9762,0.057974,-77.363,0.12236,0.032713,-0.99195,307.95

> view matrix models
> #3,-0.97023,0.21441,-0.11261,331.53,0.209,0.9762,0.057974,-75.632,0.12236,0.032713,-0.99195,308.31

> view matrix models
> #3,-0.97023,0.21441,-0.11261,331.36,0.209,0.9762,0.057974,-76.955,0.12236,0.032713,-0.99195,304.59

> view matrix models
> #3,-0.97023,0.21441,-0.11261,329.38,0.209,0.9762,0.057974,-76.165,0.12236,0.032713,-0.99195,304.47

> ui mousemode right ""rotate selected models""

> view matrix models
> #3,-0.97363,0.2243,0.041623,298.08,0.2256,0.97376,0.029771,-73.351,-0.033853,0.038377,-0.99869,334.3

> fitmap #3 inMap #2

Fit map cryosparc_P18_J28_011_volume_map_sharp (2).mrc in map
J155_ResolveMap.mrc using 368476 points  
correlation = 0.9203, correlation about mean = 0.8371, overlap = 2.783e+05  
steps = 196, shift = 3.94, angle = 10.4 degrees  
  
Position of cryosparc_P18_J28_011_volume_map_sharp (2).mrc (#3) relative to
J155_ResolveMap.mrc (#2) coordinates:  
Matrix rotation and translation  
-0.99864561 0.05202828 0.00005358 339.15808821  
0.05202828 0.99864561 0.00003529 -39.20548979  
-0.00005167 0.00003803 -1.00000000 335.57479560  
Axis 0.02602575 0.99966127 0.00001715  
Axis point 170.09381094 0.00000000 167.78325877  
Rotation angle (degrees) 179.99698390  
Shift along axis -30.35960997  
  

> select subtract #3

Nothing selected  

> surface dust #3 size 4.44

> volume #3 level 0.1228

> surface dust #3 size 4.44

> surface dust #3 size 4.29

> surface dust #3 size 6.59

> volume subtract #3 #2

Opened volume difference as #4, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32  

> volume #4 level 1.57

> volume subtract #2 #3

Opened volume difference as #5, grid size 143,143,172, pixel 0.74,0.74,0.74,
shown at step 1, values float32  

> close #5

> close #4

> volume #2 level 0.3073

> close #2

> open ""/Users/bs18klrh/Library/CloudStorage/OneDrive-
> UniversityofLeeds/Research_Postgrad/EM/Model_Building/300323
> AM237/J51_finalmap.mrc""

Opened J51_finalmap.mrc as #2, grid size 432,432,432, pixel 0.731, shown at
level 0.086, step 2, values float32  

> close #2

> open ""/Users/bs18klrh/Downloads/cryosparc_P35_J163_013_volume_map_sharp
> (5).mrc""

Opened cryosparc_P35_J163_013_volume_map_sharp (5).mrc as #2, grid size
432,432,432, pixel 0.74, shown at level 0.0854, step 2, values float32  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume #2 step 1

> volume #2 level 0.1798

> volume #2 level 0.1204

> volume #2 level 0.1588

> surface dust #3 size 6.59

> surface dust #2 size 4.44

> volume subtract #2 #3

Opened volume difference as #4, grid size 432,432,432, pixel 0.74, shown at
step 1, values float32  

> surface dust #4 size 4.44

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> volume subtract #3 #2

Opened volume difference as #5, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32  

> volume #5 level 0.1765

> surface dust #5 size 4.44

> volume #5 level 0.1429

> volume #5 color #ff85ff

> show #!2 models

> show #!3 models

> hide #!1 models

> show #!5 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #!5 models

> show #!4 models

> show #!5 models

> hide #!3 models

> hide #!4 models

> hide #!5 models

> show #!3 models

> show #!2 models

> volume #2 level 0.198

> volume #3 level 0.2239

> volume #2 level 0.3014

> volume #3 level 0.2836

> show #!5 models

> volume #5 level 0.1671

> hide #!3 models

> show #!4 models

> hide #!5 models

> show #!1 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> show #!3 models

> hide #!4 models

> hide #!3 models

> volume #2 level 0.2372

> show #!3 models

> volume #3 level 0.2317

> show #!4 models

> show #!5 models

> hide #!2 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> volume #4 level 0.2147

> show #!2 models

> volume #2 level 0.2907

> volume #3 level 0.1928

> select add #5

3 models selected  

> select subtract #5

Nothing selected  

> select add #5

3 models selected  

> close #5

> select add #4

3 models selected  

> close #4

> volume #2 level 0.1618

> ui tool show ""Fit in Map""

> fitmap #2 inMap #3

Fit map cryosparc_P35_J163_013_volume_map_sharp (5).mrc in map
cryosparc_P18_J28_011_volume_map_sharp (2).mrc using 284760 points  
correlation = 0.96, correlation about mean = 0.8512, overlap = 3.923e+04  
steps = 48, shift = 0.0945, angle = 0.0519 degrees  
  
Position of cryosparc_P35_J163_013_volume_map_sharp (5).mrc (#2) relative to
cryosparc_P18_J28_011_volume_map_sharp (2).mrc (#3) coordinates:  
Matrix rotation and translation  
-0.99859895 0.05291629 0.00008081 340.58660877  
0.05291629 0.99859895 -0.00007073 21.37572228  
-0.00008444 -0.00006636 -0.99999999 335.50177297  
Axis 0.02646920 0.99964963 -0.00003503  
Axis point 170.01724085 0.00000000 167.74423779  
Rotation angle (degrees) 179.99526449  
Shift along axis 30.37153548  
  

> volume #3 level 0.2228

> volume #2 level 0.2201

> volume #2 color #ffb2b280

> volume #3 color #ffffb282

> ui tool show ""Side View""

> volume subtract #3 #2

Opened volume difference as #4, grid size 512,512,512, pixel 0.74, shown at
step 1, values float32  

> volume #4 level 0.1698

> ui tool show ""Hide Dust""

> surface dust #4 size 4.44

> volume #4 level 0.1288

> volume #4 level 0.08379

> volume #4 level 0.1142

> volume #4 level 0.1526

> hide #!1 models

> show #!1 models

> select add #1

22580 atoms, 23112 bonds, 28 pseudobonds, 2696 residues, 3 models selected  

> ui mousemode right ""translate selected models""

> view matrix models #1,1,0,0,0.068897,0,1,0,-0.094972,0,0,1,1.7756

> view matrix models #1,1,0,0,0.80147,0,1,0,-0.52854,0,0,1,2.2016

> view matrix models #1,1,0,0,0.35242,0,1,0,-1.9022,0,0,1,2.2569

> view matrix models #1,1,0,0,0.091042,0,1,0,-2.0422,0,0,1,4.3565

> view matrix models #1,1,0,0,0.28916,0,1,0,-0.34771,0,0,1,1.6703

> view matrix models #1,1,0,0,-0.23796,0,1,0,-0.29813,0,0,1,1.0237

> select subtract #1

Nothing selected  

> undo


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M3
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.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: Mac
      Model Identifier: Mac15,3
      Model Number: Z1C8000FDB/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 18 days, 3 hours, 2 minutes

Graphics/Displays:

    Apple M3:

      Chipset Model: Apple M3
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        PLX2283H-DP:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes


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-StarMap: 1.2.15
    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
    pyqtgraph: 0.13.7
    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
    Send2Trash: 1.8.3
    SEQCROW: 1.8.14
    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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX