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Opened 3 weeks ago
Closed 3 weeks ago
#19808 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 (last modified by )
The following bug report has been submitted:
Platform: macOS-15.7.1-arm64-arm-64bit
ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Current thread 0x000000020789a140 (most recent call first):
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 368 in event_loop
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1057 in init
File "/Applications/ChimeraX-1.10.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1220 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.xtc_utils, openmm.app.internal.compiled, psutil._psutil_osx, psutil._psutil_posix, 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, PIL._imaging, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, cython.cimports.libc.math, 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._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._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct (total: 120)
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"procLaunch" : "2026-02-04 13:02:25.8609 -0500",
"procStartAbsTime" : 21061986312168,
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"codeSigningFlags" : 570491649,
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],
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> color sel byhetero
> select #2/A:70,93,94,146,147
48 atoms, 49 bonds, 5 residues, 1 model selected
> color sel byhetero
> show sel atoms
> style sel stick
Changed 48 atom styles
> cofr sel
> select #2/A:70,93,94,146,147,115
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel stick
Changed 58 atom styles
> color sel byhetero
> select #1/A:70,93,94,146,147,115
58 atoms, 59 bonds, 6 residues, 1 model selected
> show sel atoms
> color sel byhetero
> mmaker #1/A:70,93,94,146,147,115 to #2/A
Parameters
---
Chain pairing | bb
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 merged_real_space_refined_014.pdb, chain A (#2) with
merged_ivc_apo_refine_007.pdb, chain A (#1), sequence alignment score = 40
RMSD between 6 pruned atom pairs is 0.637 angstroms; (across all 6 pairs:
0.637)
> select #1/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel byhetero
> select #1/A:159, #2/A:159
Expected an objects specifier or a keyword
> show sel atoms
> select #2/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 9 atom styles
> color sel byhetero
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> color #1 #eceeedff
> open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC
> apo/merged_ivc_apo_refine_008.pdb"
Summary of feedback from opening /Users/xuchengtao/Documents/Building models
undergoing/20260114 IVC apo/merged_ivc_apo_refine_008.pdb
---
warning | Start residue of secondary structure not found: HELIX 149 149 ILE P 16 ILE P 30 1 15
Chain information for merged_ivc_apo_refine_008.pdb #3
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E F G H | No description available
I | No description available
J | No description available
K L M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
> mmaker #3 to #1
Parameters
---
Chain pairing | bb
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 merged_ivc_apo_refine_007.pdb, chain A (#1) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 2572.9
RMSD between 504 pruned atom pairs is 0.004 angstroms; (across all 504 pairs:
0.004)
> style sel stick
Changed 9 atom styles
> hide sel atoms
> undo
> hide #!3 models
> select add #2
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> select subtract #2
Nothing selected
> select add #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> hide #3
> show #!3 models
> select subtract #3
Nothing selected
> show #3/A:70, 115,146,147,93,94,159
> style stick
Changed 93851 atom styles
> hide #!1 models
> color #3 #e1e4eeff
> color #3 #b2b5bdff
> mmaker #3/A:70, 115,146,147,93,94,159 to #2/A
Parameters
---
Chain pairing | bb
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 merged_real_space_refined_014.pdb, chain A (#2) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 45.3
RMSD between 7 pruned atom pairs is 0.851 angstroms; (across all 7 pairs:
0.851)
> show #1/A:97
> show #!1 models
> hide #!1 models
> show #2/A:97
> show #3/A:97
> hide #!3 models
> show #!3 models
> open "/Users/xuchengtao/Documents/Building models
> undergoing/20251003IVC/20251222 Xiaomeng AI
> IVC/cryosparc_P6_J91_004_volume_map.mrc"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.0524, step 2, values float32
> volume #4 step 1
> volume #4 level 0.1661
> ui tool show "Hide Dust"
> surface dust #4 size 11.38
> surface dust #4 size 12.58
> surface dust #4 size 10.12
> volume #4 color #b2b2b2ab
> ui tool show "Color Actions"
> color light sky blue
> hide #!4 models
> hide #!3 models
> show #!3 models
> select #2
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> color sel byhetero
> select #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> ui tool show "Color Actions"
> color sel pink
> color sel byhetero
> select subtract #3
Nothing selected
> open "/Users/xuchengtao/Documents/Building models undergoing/20260114 IVC
> apo/cryosparc_P38_J47_006_volume_map.mrc"
Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512,
pixel 1.07, shown at level 0.0338, step 2, values float32
> volume #5 step 1
> surface dust #5 size 9.46
> mmaker #5 to #4
No 'to' model specified
> mmaker #5 to #3
No molecules/chains to match specified
> surface dust #5 size 9.3
> surface dust #5 size 11.38
> surface dust #5 size 9.62
> surface dust #5 size 10.29
> surface dust #5 size 13.23
> volume #5 level 0.09228
> ui tool show "Fit in Map"
> ui mousemode right "translate selected models"
> select add #5
2 models selected
> view matrix models
> #5,-0.97381,-0.031588,0.22517,490.36,-0.071884,0.98228,-0.17308,73.711,-0.21571,-0.18473,-0.95882,664.68
> view matrix models
> #5,-0.97381,-0.031588,0.22517,436.09,-0.071884,0.98228,-0.17308,0.20124,-0.21571,-0.18473,-0.95882,557.69
> volume #5 level 0.1173
> view matrix models
> #5,-0.93478,0.30346,0.18464,345.57,0.2887,0.95188,-0.10282,-106.34,-0.20696,-0.042808,-0.97741,523.25
> fitmap #5 inMap #4
Fit map cryosparc_P38_J47_006_volume_map.mrc in map
cryosparc_P6_J91_004_volume_map.mrc using 310271 points
correlation = 0.9347, correlation about mean = 0.7922, overlap = 1.556e+04
steps = 220, shift = 18.3, angle = 17.3 degrees
Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to
cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.97760466 0.20023007 -0.06478454 435.09526992
0.19862444 0.97960384 0.03040797 -118.87262867
0.06955178 0.01685918 -0.99743587 434.81572276
Axis -0.10034105 -0.99488204 -0.01189115
Axis point 216.14301063 0.00000000 225.62653040
Rotation angle (degrees) 176.12880575
Shift along axis 69.43586944
> view matrix models
> #5,-0.99043,0.12889,-0.049357,453.43,0.1291,0.99163,-0.0012337,-93.971,0.048785,-0.0075941,-0.99878,447.49
> volume #5 level 0.1674
> view matrix models
> #5,-0.98693,0.15429,-0.046578,444.85,0.15422,0.98802,0.0051166,-101.57,0.04681,-0.0021338,-0.9989,446.59
> view matrix models
> #5,-0.99436,0.088993,0.057707,435.97,0.099112,0.97336,0.20674,-137.79,-0.037772,0.21129,-0.97669,405.88
> view matrix models
> #5,-0.99438,0.087718,0.059321,435.88,0.098341,0.97272,0.21009,-138.33,-0.039274,0.21474,-0.97588,405.13
> undo
> view matrix models
> #5,-0.98265,0.16324,-0.088032,452.62,0.16414,0.98643,-0.0029871,-101.62,0.08635,-0.017385,-0.99611,439.18
> volume #5 level 0.2085
> color sel pink
> volume #5 color #ffc0cbad
> volume #4 level 0.12
> show #2/B
> select #2/B
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> ui tool show "Color Actions"
> color sel slate gray
> hide #!3 models
> volume #4 level 0.13
> volume #4 level 0.14
> matchmaker #4 to #2
No molecules/chains to match specified
> select add #2
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> select subtract #2
Nothing selected
> hide #!2 models
> close #2
> open "/Users/xuchengtao/Documents/Building models
> undergoing/20251003IVC/20251222 Xiaomeng AI
> IVC/merged_real_space_refined_015.pdb"
Chain information for merged_real_space_refined_015.pdb #2
---
Chain | Description
A | No description available
C H I J K L | No description available
D | No description available
E | No description available
F | No description available
G | No description available
M | No description available
N O P Q R | No description available
S | No description available
> hide #2
> combine #2
> color #2 lightskyblue
> color #6 lightskyblue
> select #2/A:70,93,94,97,115,146,159
66 atoms, 64 bonds, 7 residues, 1 model selected
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 66 atom styles
> color sel byhetero
> select #2/B
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> show sel atoms
> color sel gray
> ui tool show "Color Actions"
> color sel slate gray
> volume #4 color #87cefa27
> volume #4 color #87cefa26
> lighting full
> lighting soft
> lighting full
> hide #2/A:94
> select #5/A:94,147
Nothing selected
> show #5/A:94,147 & ~@N,C,O
> show #!5 models
> hide #!5 models
> show #6/A:94,147 & ~@N,C,O
> select #6/A
4478 atoms, 4580 bonds, 1 pseudobond, 550 residues, 2 models selected
> style sel stick
Changed 4478 atom styles
> color sel byhetero
> select add #6
30525 atoms, 31271 bonds, 7 pseudobonds, 3696 residues, 3 models selected
> select subtract #6
Nothing selected
> combine #3
> hide #3
> hide #7
> show #!5 models
> volume #5 level 0.1566
> volume #5 color #ffc0cb2b
> select #3/A:70,93,97,115,146,159
58 atoms, 56 bonds, 6 residues, 1 model selected
> show (#2,4,6-7 & sidechain) target ab
> select #3/A:70,93,97,115,146,159
58 atoms, 56 bonds, 6 residues, 1 model selected
> show #3/A:70,93,97,115,146,159& ~@N,,C,O
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #3/A:70,93,97,115,146,159& ~@N,C,O
> show #!3 models
> hide #2/A:97
> hide #3/A:97
> mmaker #3/A:70,93,94,115 to #2/A
Parameters
---
Chain pairing | bb
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 merged_real_space_refined_015.pdb, chain A (#2) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 26.4
RMSD between 4 pruned atom pairs is 0.646 angstroms; (across all 4 pairs:
0.646)
> mmaker #3/A:70,93,94,115,146 to #2/A
Parameters
---
Chain pairing | bb
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 merged_real_space_refined_015.pdb, chain A (#2) with
merged_ivc_apo_refine_008.pdb, chain A (#3), sequence alignment score = 33.2
RMSD between 5 pruned atom pairs is 0.680 angstroms; (across all 5 pairs:
0.680)
> close #7
> combine #3
> hide #7
> show #7/A:94,147 & ~@N,CA,C,O
> show #7/A:94,147 & ~@N,,C,O
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show #7/A:94,147 & ~@N,C,O
> select add #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> select subtract #3
Nothing selected
> hide #!2 models
> show #!2 models
> hide #!4 models
> show #!5 models
> show #!4 models
> select add #5
2 models selected
> view matrix models
> #5,-0.97841,0.20197,-0.043758,428.89,0.20245,0.97927,-0.0068224,-109.08,0.041473,-0.015534,-0.99902,451.71
> undo
> select subtract #5
Nothing selected
> select add #4
2 models selected
> select subtract #4
Nothing selected
> hide #!4 models
> hide #!2 models
> hide #!6 models
> select add #5
2 models selected
> view matrix models
> #5,-0.95877,0.093992,-0.2682,514.11,0.090359,0.99557,0.025885,-91.881,0.26944,0.00058378,-0.96302,375.36
> volume #5 level 0.1727
> view matrix models
> #5,-0.97116,0.2003,-0.12934,450.76,0.20327,0.97907,-0.010053,-108.32,0.12462,-0.036052,-0.99155,432.49
> cofr @3/A
> cofr #3/A
> view matrix models
> #5,-0.96897,0.21997,-0.11274,440.16,0.22373,0.97441,-0.021689,-109.42,0.10508,-0.046238,-0.99339,440.91
> view matrix models
> #5,-0.98673,0.16214,0.0085692,427.41,0.16178,0.98627,-0.033106,-92.633,-0.013819,-0.03128,-0.99942,470.88
> view matrix models
> #5,-0.99996,-0.0010926,-0.0093869,480.02,-0.0013883,0.9995,0.031557,-69.497,0.0093478,0.031569,-0.99946,447.61
> view matrix models
> #5,-0.99994,-0.010838,0.0021348,479.5,-0.010849,0.99993,-0.0051597,-56.987,-0.0020787,-0.0051825,-0.99998,460.79
> view matrix models
> #5,-0.99926,-0.0041216,0.038311,467.59,-0.0039274,0.99998,0.0051435,-61.705,-0.038331,0.0049892,-0.99925,467.71
> view matrix models
> #5,-0.99926,-0.0041216,0.038311,467.58,-0.0039274,0.99998,0.0051435,-61.937,-0.038331,0.0049892,-0.99925,467.37
> volume #5 level 0.16
> volume #5 color #ffc0cbd6
> volume #5 level 0.17
> view matrix models
> #5,-0.9987,-0.049666,0.011361,487.1,-0.049572,0.99873,0.0084327,-50.07,-0.011765,0.0078586,-0.9999,459.55
> view matrix models
> #5,-0.9987,-0.049666,0.011361,486.96,-0.049572,0.99873,0.0084327,-49.824,-0.011765,0.0078586,-0.9999,459.82
> volume #5 level 0.15
> volume #5 level 0.175
> view matrix models
> #5,-0.9987,-0.049666,0.011361,487.47,-0.049572,0.99873,0.0084327,-50.955,-0.011765,0.0078586,-0.9999,458.34
> view matrix models
> #5,-0.99639,-0.068145,-0.0506,508.8,-0.077294,0.97481,0.20922,-91.913,0.035067,0.21238,-0.97656,383.96
> undo
> view matrix models
> #5,-0.90445,-0.37278,0.20738,495.44,-0.36083,0.92786,0.094206,29.42,-0.22754,0.010378,-0.97371,509.22
> view matrix models
> #5,-0.90445,-0.37278,0.20738,496,-0.36083,0.92786,0.094206,27.507,-0.22754,0.010378,-0.97371,509.24
> view matrix models
> #5,-0.90445,-0.37278,0.20738,506.69,-0.36083,0.92786,0.094206,29.176,-0.22754,0.010378,-0.97371,509.83
> view matrix models
> #5,-0.90435,-0.36259,0.22513,499.05,-0.35913,0.93151,0.05762,37.745,-0.2306,-0.028742,-0.97262,520.93
> view matrix models
> #5,-0.90435,-0.36259,0.22513,500.51,-0.35913,0.93151,0.05762,36.126,-0.2306,-0.028742,-0.97262,518.8
> view matrix models
> #5,-0.90384,-0.33625,0.2646,482.45,-0.35563,0.93422,-0.027601,57.769,-0.23792,-0.11905,-0.96396,542.81
> view matrix models
> #5,-0.90384,-0.33625,0.2646,487.46,-0.35563,0.93422,-0.027601,49.35,-0.23792,-0.11905,-0.96396,540.04
> view matrix models
> #5,-0.9033,-0.31727,0.28876,475.58,-0.3537,0.93169,-0.082759,64.605,-0.24278,-0.17689,-0.95382,554.21
> view matrix models
> #5,-0.9033,-0.31727,0.28876,479.2,-0.3537,0.93169,-0.082759,57.847,-0.24278,-0.17689,-0.95382,553.3
> volume #5 level 0.1947
> volume #5 level 0.175
> show #!2 models
> hide #!2 models
> show #!4 models
> view matrix models
> #5,-0.90789,-0.32005,0.27076,486.12,-0.35802,0.92795,-0.1036,65.738,-0.21809,-0.19099,-0.95706,551.27
> fitmap #5 inMap #4
Fit map cryosparc_P38_J47_006_volume_map.mrc in map
cryosparc_P6_J91_004_volume_map.mrc using 186216 points
correlation = 0.9452, correlation about mean = 0.7716, overlap = 1.379e+04
steps = 380, shift = 27.5, angle = 38 degrees
Position of cryosparc_P38_J47_006_volume_map.mrc (#5) relative to
cryosparc_P6_J91_004_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
-0.97747656 0.20090883 -0.06461583 434.82603912
0.19929299 0.97946158 0.03061556 -119.07093066
0.06943966 0.01704851 -0.99744046 434.80014734
Axis -0.10068315 -0.99484628 -0.01199138
Axis point 216.05419591 0.00000000 225.60664569
Rotation angle (degrees) 176.13677177
Shift along axis 69.46376469
> hide #!4 models
> volume #5 level 0.1589
> volume #5 level 0.15
> view matrix models
> #5,-0.97451,0.21473,-0.064928,430.36,0.21213,0.97622,0.044705,-125.65,0.072984,0.029792,-0.99689,430.23
> undo
> view matrix models
> #5,-0.97748,0.20091,-0.064616,436.21,0.19929,0.97946,0.030616,-119.26,0.06944,0.017049,-0.99744,436.08
> view matrix models
> #5,-0.97239,0.22414,-0.065027,428.65,0.22083,0.9738,0.054308,-130.26,0.075496,0.038448,-0.9964,428.35
> view matrix models
> #5,-0.97239,0.22414,-0.065027,428.82,0.22083,0.9738,0.054308,-127.24,0.075496,0.038448,-0.9964,428.69
> undo
> hide #!4 models
> volume #5 level 0.1661
> view matrix models
> #5,-0.96662,0.25053,-0.05365,415.47,0.24919,0.96798,0.030408,-129.49,0.05955,0.016024,-0.9981,437.95
> view matrix models
> #5,-0.96653,0.25013,-0.056982,416.46,0.2497,0.96821,0.01465,-125.38,0.058835,-6.834e-05,-0.99827,442.54
> view matrix models
> #5,-0.96653,0.25013,-0.056982,416.26,0.2497,0.96821,0.01465,-126.49,0.058835,-6.834e-05,-0.99827,443.79
> undo
> view matrix models
> #5,-0.97268,0.22126,-0.070311,429.58,0.21796,0.97459,0.051693,-128.6,0.079962,0.034956,-0.99618,426.75
> view matrix models
> #5,-0.97268,0.22126,-0.070311,430.14,0.21796,0.97459,0.051693,-126.95,0.079962,0.034956,-0.99618,427.81
> view matrix models
> #5,-0.97268,0.22126,-0.070311,430.12,0.21796,0.97459,0.051693,-127.05,0.079962,0.034956,-0.99618,427.18
> volume #5 level 0.1589
> view matrix models
> #5,-0.97111,0.22523,-0.078833,430.95,0.22249,0.97403,0.042032,-125.48,0.086252,0.023278,-0.996,428.57
> undo
> view matrix models
> #5,-0.96202,0.25857,-0.087537,421.85,0.25149,0.96419,0.084256,-142.27,0.10619,0.059042,-0.99259,412.55
> view matrix models
> #5,-0.96202,0.25857,-0.087537,422.58,0.25149,0.96419,0.084256,-138.97,0.10619,0.059042,-0.99259,414.88
> volume #5 level 0.1446
> undo
> volume #5 level 0.1607
> volume #5 level 0.1446
> view matrix models
> #5,-0.9737,0.21948,-0.061119,428.33,0.21816,0.97552,0.027604,-120.53,0.065681,0.013544,-0.99775,437.95
> view matrix models
> #5,-0.9737,0.21948,-0.061119,429.45,0.21816,0.97552,0.027604,-123.69,0.065681,0.013544,-0.99775,436.46
> view matrix models
> #5,-0.9737,0.21948,-0.061119,430.1,0.21816,0.97552,0.027604,-123.83,0.065681,0.013544,-0.99775,436.76
> view matrix models
> #5,-0.96936,0.23489,-0.071894,427.76,0.23263,0.9718,0.038497,-129.84,0.07891,0.020593,-0.99667,430.93
> view matrix models
> #5,-0.96936,0.23489,-0.071894,427.42,0.23263,0.9718,0.038497,-128.58,0.07891,0.020593,-0.99667,431.63
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.29,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.72
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.23,0.23421,0.97154,0.035438,-127.81,0.091031,0.014376,-0.99574,429.7
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.59,0.23421,0.97154,0.035438,-127.05,0.091031,0.014376,-0.99574,429.19
> view matrix models
> #5,-0.96792,0.23643,-0.085073,430.19,0.23421,0.97154,0.035438,-128.03,0.091031,0.014376,-0.99574,428.89
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.53,0.23421,0.97154,0.035438,-128.27,0.091031,0.014376,-0.99574,428.38
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.63,0.23421,0.97154,0.035438,-128.15,0.091031,0.014376,-0.99574,429.1
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.12,0.091031,0.014376,-0.99574,428.9
> view matrix models
> #5,-0.96958,0.23531,-0.067362,425.42,0.23325,0.97171,0.037075,-128.3,0.074181,0.020235,-0.99704,432.33
> view matrix models
> #5,-0.9663,0.24851,-0.0672,420.91,0.24554,0.96813,0.049372,-134.15,0.077327,0.031207,-0.99652,428.36
> view matrix models
> #5,-0.9663,0.24851,-0.0672,422.24,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.54
> view matrix models
> #5,-0.9663,0.24851,-0.0672,422.17,0.24554,0.96813,0.049372,-132.3,0.077327,0.031207,-0.99652,429.18
> view matrix models
> #5,-0.9663,0.24851,-0.0672,422.48,0.24554,0.96813,0.049372,-132.23,0.077327,0.031207,-0.99652,429.48
> view matrix models
> #5,-0.96297,0.26101,-0.067585,418.3,0.25702,0.96439,0.062399,-138.01,0.081465,0.042718,-0.99576,425.02
> view matrix models
> #5,-0.96297,0.26101,-0.067585,418.54,0.25702,0.96439,0.062399,-136.93,0.081465,0.042718,-0.99576,425.35
> undo
> volume #5 level 0.1339
> volume #5 color #ffc0cb29
> volume #5 color #ffc0cb61
> show #!4 models
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.64,0.23421,0.97154,0.035438,-128.16,0.091031,0.014376,-0.99574,429.11
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.59,0.23421,0.97154,0.035438,-128.26,0.091031,0.014376,-0.99574,429.29
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.69,0.23421,0.97154,0.035438,-128.37,0.091031,0.014376,-0.99574,429.46
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.4,0.23421,0.97154,0.035438,-128.44,0.091031,0.014376,-0.99574,429.31
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.37,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.16
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.43,0.23421,0.97154,0.035438,-128.61,0.091031,0.014376,-0.99574,429.7
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.22,0.23421,0.97154,0.035438,-128.65,0.091031,0.014376,-0.99574,429.53
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.16,0.23421,0.97154,0.035438,-128.43,0.091031,0.014376,-0.99574,429.54
> hide #!3 models
> show #!3 models
> hide #!4 models
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.36,0.23421,0.97154,0.035438,-128.09,0.091031,0.014376,-0.99574,429.64
> view matrix models
> #5,-0.96792,0.23643,-0.085073,429.21,0.23421,0.97154,0.035438,-127.78,0.091031,0.014376,-0.99574,429.58
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.37,0.23421,0.97154,0.035438,-127.04,0.091031,0.014376,-0.99574,429.41
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.35,0.23421,0.97154,0.035438,-126.11,0.091031,0.014376,-0.99574,429.73
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.3,0.23421,0.97154,0.035438,-126,0.091031,0.014376,-0.99574,429.7
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.24,0.23421,0.97154,0.035438,-126.37,0.091031,0.014376,-0.99574,429.57
> volume #5 level 0.1464
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.2,0.23421,0.97154,0.035438,-126.21,0.091031,0.014376,-0.99574,429.4
> view matrix models
> #5,-0.96792,0.23643,-0.085073,428.13,0.23421,0.97154,0.035438,-125.77,0.091031,0.014376,-0.99574,429.31
> show #3/T
> select #3/T
2 atoms, 2 residues, 1 model selected
> style sel sphere
Changed 2 atom styles
> ui tool show "Color Actions"
> color sel slate gray
> select add #3
31663 atoms, 32359 bonds, 18 pseudobonds, 3889 residues, 2 models selected
> select subtract #3
Nothing selected
> ui tool show "Side View"
> hide #!3 models
> hide #!5 models
> hide #!7 models
> show #!4 models
> show #!6 models
> show #!2 models
> volume #4 level 0.12
> volume #4 level 0.125
> lighting full
> lighting soft
> lighting simple
> lighting full
> lighting flat
> lighting full
> lighting simple
> lighting full
> volume #4 level 0.13
> save /Users/xuchengtao/Desktop/image275.png supersample 3
> hide #!4 models
> hide #!2 models
> show #!3 models
> show #!5 models
> hide #!6 models
> show #!7 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"
> save /Users/xuchengtao/Desktop/image276.png supersample 3
> hide #!3 models
> hide #!5 models
> hide #!7 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #3/T
> show #!4 models
> hide #!4 models
> show #!2 models
> show #!6 models
> show #2/A:86-96 cartoons
> cartoon style #2-3,6-7 modeHelix tube sides 20
> cartoon style (#2-3,6-7 & coil) xsection oval
> cartoon style #2-3,6-7 xsection barbell modeHelix default
> cartoon style #2-3,6-7 modeHelix tube sides 20
> show #2/A:136-160 cartoons
> combine #7
> color #8 white
> color #8 #ffffffb4
> color #8 #ffffff82
> color #8 #ffffff80
> color #8 #f5f4f680
> show #8/A:136-160 cartoons
> show #8/A:86-96 cartoons
> show #8/A:136-180 cartoons
> show #2/A:136-180 cartoons
> show #2/A:136-160 cartoons
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"
> hide #2/A:161-180 cartoons
> hide #8/A:161-180 cartoons
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> hide #8/A:147
> hide #8/A:94]
> hide #8/A:94
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> lighting full
> lighting soft
> hide #!2 models
> hide #!6 models
> show #!2 models
> show #!6 models
> lighting shadows true intensity 0.5
> lighting full
> lighting shadows false
> save /Users/xuchengtao/Desktop/image277.png supersample 3
> ui tool show Distances
> select #2/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:159
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #3/A:159, #2/A:159
Expected an objects specifier or a keyword
Exactly two atoms must be selected!
> select #2,3/A:159@CA
2 atoms, 2 residues, 2 models selected
> distance #3/A:159@CA #2/A:159@CA
Distance between merged_ivc_apo_refine_008.pdb #3/A GLU 159 CA and
merged_real_space_refined_015.pdb #2/A GLU 159 CA: 2.124Å
> undo
> ~distance #3/A:159@CA #2/A:159@CA
> lighting shadows true
> lighting full
> lighting soft
> depthCue true
Unknown command: depthCue true
> depthCue true
Unknown command: depthCue true
> depthCue true
Unknown command: depthCue true
> depthCue
Unknown command: depthCue
> lighting depthCue true
> lighting depthCueStart 0.4 depthCueEnd 0.9
> lighting depthCueStart 0.4 depthCueEnd 0.8
> lighting depthCueStart 0.2 depthCueEnd 0.8
> lighting depthCueStart 0.1 depthCueEnd 0.8
> lighting depthCueStart 0.1 depthCueEnd 0.4
> lighting depthCueStart 0.2 depthCueEnd 0.4
> lighting depthCueStart 0.3 depthCueEnd 0.4
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting depthCueStart 0.3 depthCueEnd 0.4
> lighting depthCueStart 0.4 depthCueEnd 0.9
> lighting depthCueStart 0.4 depthCueEnd 0.5
> lighting depthCueStart 0.3 depthCueEnd 0.5
> lighting depthCueStart 0.3 depthCueEnd 0.4
> lighting depthCueStart 0.4
> lighting depthCueStart 0.9
> lighting depthCueStart 0.
> lighting depthCueStart 0.5
> lighting depthCueStart 0.4
> show #!2 models
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC manuscript/IVC_DNA_bound/IVC_DNAbound_PAM6.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.227, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc copy as #1, grid size 384,384,384,
pixel 1.07, shown at level 0.266, step 1, values float32
Opened cryosparc_P6_J91_004_volume_map.mrc as #3, grid size 384,384,384, pixel
1.07, shown at level 0.153, step 1, values float32
> view name session-start
opened ChimeraX session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_6.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.13, step 1, values float32
Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512,
pixel 1.07, shown at level 0.146, step 1, values float32
> view name session-start
opened ChimeraX session
> open "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
Opened cryosparc_P6_J91_004_volume_map.mrc as #4, grid size 384,384,384, pixel
1.07, shown at level 0.13, step 1, values float32
Opened cryosparc_P38_J47_006_volume_map.mrc as #5, grid size 512,512,512,
pixel 1.07, shown at level 0.146, step 1, values float32
> view name session-start
opened ChimeraX session
> lighting depthCueStart 0.4 depthCueStart 0.9
Repeated keyword argument "depthCueStart"
> lighting depthCueStart 0.4 depthCueEnd 0.9
> lighting depthCueStart 0.4 depthCueEnd 0.6
> lighting depthCueStart 0.1 depthCueEnd 0.6
> lighting depthCueStart 0.2 depthCueEnd 0.6
> lighting depthCueStart 0.2 depthCueEnd 0.3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> lighting depthCueStart 0.2 depthCueEnd 0.25
> lighting depthCueStart 0.2 depthCueEnd 0.5
> lighting depthCueStart 0.2 depthCueEnd 0.25
> lighting depthCueStart 0.2 depthCueEnd 0.28
> lighting depthCueStart 0.2 depthCueEnd 0.3
> lighting depthCueStart 0.2 depthCueEnd 0.34
> save /Users/xuchengtao/Desktop/image278.png supersample 3
> save /Users/xuchengtao/Desktop/image279.png supersample 3
> lighting depthCueStart 0.2 depthCueEnd 0.33
> lighting depthCueStart 0.2 depthCueEnd 0.3
> save /Users/xuchengtao/Desktop/image280.png supersample 3
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> lighting depthCue false
> save "/Users/xuchengtao/Documents/Postdoc/4-program/Collaboration_Type IV
> with Terns/20260111 IVC
> manuscript/IVC_DNA_bound/IVC_DNAbound_HD_compare_apo_7.cxs"
> close session
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_00_00162_volume.mrc
Opened J31_class_00_00162_volume.mrc as #1, grid size 128,128,128, pixel 3.01,
shown at level 0.108, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_01_00162_volume.mrc
Opened J31_class_01_00162_volume.mrc as #2, grid size 128,128,128, pixel 3.01,
shown at level 0.126, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_02_00162_volume.mrc
Opened J31_class_02_00162_volume.mrc as #3, grid size 128,128,128, pixel 3.01,
shown at level 0.0868, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_03_00162_volume.mrc
Opened J31_class_03_00162_volume.mrc as #4, grid size 128,128,128, pixel 3.01,
shown at level 0.241, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_04_00162_volume.mrc
Opened J31_class_04_00162_volume.mrc as #5, grid size 128,128,128, pixel 3.01,
shown at level 0.105, step 1, values float32
> open
> /Users/xuchengtao/Downloads/cryosparc_P9_J31_00162_volumes/J31_class_05_00162_volume.mrc
Opened J31_class_05_00162_volume.mrc as #6, grid size 128,128,128, pixel 3.01,
shown at level 0.27, step 1, values float32
> color #1-6 lightgrey
> ui tool show "Hide Dust"
> surface dust #1 size 18.06
> surface dust #1 size 30.1
> surface dust #2 size 30.1
> surface dust #3 size 30.1
> surface dust #4 size 30.1
> surface dust #5 size 30.1
> surface dust #6 size 30.1
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> hide #!6 models
> hide #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> hide #!3 models
> hide #!2 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> show #!6 models
> show #!1 models
> show #!2 models
> show #!3 models
> show #!4 models
> show #!5 models
> hide #!5 models
> hide #!6 models
> hide #!4 models
> hide #!3 models
> hide #!2 models
> save /Users/xuchengtao/Desktop/image281.png supersample 3
> lighting full
> lighting soft
> save /Users/xuchengtao/Desktop/image282.png supersample 3
> hide #!1 models
> show #!2 models
> save /Users/xuchengtao/Desktop/image283.png supersample 3
> hide #!2 models
> show #!3 models
> save /Users/xuchengtao/Desktop/image284.png supersample 3
> hide #!3 models
> show #!4 models
> save /Users/xuchengtao/Desktop/image285.png supersample 3
> hide #!4 models
> show #!5 models
> save /Users/xuchengtao/Desktop/image286.png supersample 3
> hide #!5 models
> show #!6 models
> save /Users/xuchengtao/Desktop/image287.png supersample 3
> hide #!6 models
> open /Users/xuchengtao/Downloads/cryosparc_P9_J32_007_volume_map.mrc
Opened cryosparc_P9_J32_007_volume_map.mrc as #7, grid size 360,360,360, pixel
1.07, shown at level 0.0564, step 2, values float32
> color #7 #f4f6fcff models
> volume #7 step 1
> volume #7 level 0.07916
> surface dust #7 size 10.7
> volume #7 level 0.11
> lighting full
> volume #7 color #cecfd4
> lighting simple
> volume #7 color #a3a4a7
> color #7 lightgrey
> color #7 grey
> volume #7 color #b6b6b6
> save /Users/xuchengtao/Desktop/image288.png supersample 3
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.1 (2025-07-24)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac16,8
Model Number: Z1FF000ENLL/A
Chip: Apple M4 Pro
Total Number of Cores: 14 (10 performance and 4 efficiency)
Memory: 48 GB
System Firmware Version: 13822.1.2
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.7.1 (24G231)
Kernel Version: Darwin 24.6.0
Time since boot: 26 days, 11 hours, 19 minutes
Graphics/Displays:
Apple M4 Pro:
Chipset Model: Apple M4 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 20
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
HP 23f:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 75.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
babel: 2.17.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.6.1
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.2
ChimeraX-AddCharge: 1.5.19
ChimeraX-AddH: 2.2.7
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.20.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.4
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.7
ChimeraX-AtomicLibrary: 14.1.19
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.5.1
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.25.2
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
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: 1.4.1
ChimeraX-Hbonds: 2.5.1
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ISOLDE: 1.10.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.6.2
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.10.1
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.19
ChimeraX-ModelPanel: 1.5.1
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-MutationScores: 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: 1.14.1
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.10
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: 1.1.3
ChimeraX-ProfileGrids: 1.1.3
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.3
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.7
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.1
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
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: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.45.2
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.1.5
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.2
coverage: 7.10.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.15
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.18.0
fonttools: 4.59.0
funcparserlib: 2.0.0a0
glfw: 2.9.0
grako: 3.16.5
h5py: 3.14.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
iniconfig: 2.1.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.7
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.3
jupyter_core: 5.8.1
jupyterlab_widgets: 3.0.15
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.3.2
MarkupSafe: 3.0.2
matplotlib: 3.10.1
matplotlib-inline: 0.1.7
msgpack: 1.1.0
ndindex: 1.10.0
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.11.0
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.4.0
pip: 25.0.1
pkginfo: 1.11.1
platformdirs: 4.3.8
pluggy: 1.6.0
prompt_toolkit: 3.0.51
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.3.5
pynrrd: 1.0.0
PyOpenGL: 3.1.9
PyOpenGL-accelerate: 3.1.9
pyopenxr: 1.1.4501
pyparsing: 3.2.3
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.8.1
PyQt6-Qt6: 6.8.2
PyQt6-WebEngine-commercial: 6.8.0
PyQt6-WebEngine-Qt6: 6.8.2
PyQt6_sip: 13.10.0
pytest: 8.4.1
pytest-cov: 6.2.1
python-dateutil: 2.9.0.post0
pytz: 2025.2
pyzmq: 27.0.0
qtconsole: 5.5.2
QtPy: 2.4.3
qtshim: 1.1
RandomWords: 0.4.0
requests: 2.32.3
roman-numerals-py: 3.1.0
scipy: 1.14.0
setuptools: 78.1.0
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.7
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.1.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.7.1
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.4
tornado: 6.5.1
traitlets: 5.14.3
typing_extensions: 4.14.1
tzdata: 2025.2
urllib3: 2.5.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.14
Change History (2)
comment:1 by , 3 weeks ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 3 weeks ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
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The ChimeraX bug report panel said what we know about this crash:
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX."
ChimeraX 1.11 uses a newer version of Qt window toolkit where we have not seen this crash. So try the current 1.11 version.