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Opened 7 days ago
Closed 7 days ago
#19428 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-15.6.1-arm64-arm-64bit
ChimeraX Version: 1.10.dev202503130118 (2025-03-13 01:18:56 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: Bus error
Current thread 0x00000001f46c60c0 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 339 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, cython.cimports.libc.math, 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._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, chimerax.pdb_lib._load_libs, chimerax.surface._surface, 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, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imaging, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lxml._elementpath, lxml.etree (total: 103)
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"codeSigningMonitor" : 2,
"incident" : "E07982F0-5CB5-4132-91F2-109277B58606",
"pid" : 31882,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-11-24 15:15:37.4438 -0800",
"procStartAbsTime" : 756994801520,
"procExitAbsTime" : 885325116485,
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"appleIntelligenceStatus" : {"state":"available"},
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1200_final_volume_series
> (5)/J1200_class_00_final_volume.mrc"
Opened J1200_class_00_final_volume.mrc as #1, grid size 192,192,192, pixel
2.28, shown at level 0.0447, step 1, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1200_final_volume_series
> (5)/J1200_class_01_final_volume.mrc"
Opened J1200_class_01_final_volume.mrc as #2, grid size 192,192,192, pixel
2.28, shown at level 0.0435, step 1, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1200_final_volume_series
> (5)/J1200_class_02_final_volume.mrc"
Opened J1200_class_02_final_volume.mrc as #3, grid size 192,192,192, pixel
2.28, shown at level 0.0428, step 1, values float32
> surface dust #1 size 22.8
> surface dust #2 size 22.8
> surface dust #3 size 22.8
> volume #1 level 0.06013
> volume #2 level 0.05754
> volume #3 level 0.08757
> tile
3 models tiled
> volume #1 level 0.07212
> volume #2 level 0.07157
> volume #3 level 0.09006
> select add #2
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.41841,0.90777,0.029918,109.67,-0.89346,0.40544,0.19324,271.02,0.16328,-0.10758,0.9807,-9.3401
> view matrix models
> #2,-0.94347,0.32584,0.060744,519.71,-0.29316,-0.90584,0.30578,392.28,0.15466,0.27069,0.95016,-80.322
> ui mousemode right translate
> volume #2 level 0.09184
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.50371,-0.858,0.10053,680.2,0.84388,-0.46383,0.26967,56.593,-0.18475,0.22067,0.95769,2.3273
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.50371,-0.858,0.10053,598.04,0.84388,-0.46383,0.26967,61.367,-0.18475,0.22067,0.95769,-11.724
> ui mousemode right translate
> select subtract #2
Nothing selected
> select add #3
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.12379,0.97329,0.19335,162.7,-0.98238,0.092707,0.1623,354.17,0.14004,-0.21004,0.96761,-12.745
> ui mousemode right translate
> select subtract #3
Nothing selected
> graphics silhouettes true
> lighting shadows true
> lighting soft
> set bgColor white
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/zrizvi/Desktop/movie4.mp4
Movie saved to /Users/zrizvi/Desktop/movie4.mp4
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo lab/with
> snrnp ab initio.cxs" includeMaps true
> set bgColor white
> ui mousemode right "rotate selected models"
> ui mousemode right translate
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo
> lab/alphafold and cryo structures-IMPO .cxs"
Opened cryosparc_P391_J1119_006_volume_map (1).mrc as #3, grid size
400,400,400, pixel 0.731, shown at level 0.0347, step 1, values float32
Opened 7os1 map 20 as #7, grid size 32,32,40, pixel 6.67, shown at step 1,
values float32
Opened cryosparc_P391_J1144_010_volume_map (3).mrc as #8, grid size
500,500,500, pixel 0.731, shown at level 0.0185, step 1, values float32
Opened combination of 8d7z and 7os1 map 15 as #6, grid size 46,48,51, pixel 5,
shown at level 0.0562, step 1, values float32
Opened snrnp_fullmask.mrc as #9, grid size 500,500,500, pixel 0.731, shown at
level 0.0562, step 1, values float32
Opened combination map 15 as #11, grid size 39,43,47, pixel 5, shown at level
0.0543, step 1, values float32
Opened snrnp_halfmask.mrc as #12, grid size 500,500,500, pixel 0.731, shown at
level 0.0543, step 1, values float32
Opened cryosparc_P391_J1237_008_volume_map (1).mrc as #13, grid size
500,500,500, pixel 0.731, shown at level 0.0201, step 1, values float32
Opened cryosparc_P391_J1238_010_volume_map (1).mrc as #14, grid size
500,500,500, pixel 0.731, shown at level 0.0267, step 1, values float32
Opened cryosparc_P391_J1238_010_volume_map (1).mrc z flip as #16, grid size
500,500,500, pixel 0.731, shown at level 0.0267, step 1, values float32
Opened emdb 13045 as #17, grid size 336,336,336, pixel 0.832, shown at level
0.3, step 2, values float32
Log from Mon Nov 24 16:39:31 2025UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> set bgColor transparent
Log from Tue Oct 28 15:23:27 2025UCSF ChimeraX version: 1.10.dev202503130118
(2025-03-13)
© 2016-2025 Regents of the University of California. All rights reserved.
> open "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo
> lab/alphafold and cryo structures .cxs"
Opened cryosparc_P391_J1119_006_volume_map (1).mrc as #3, grid size
400,400,400, pixel 0.731, shown at level 0.0347, step 1, values float32
Opened combination map 20 as #6, grid size 41,40,47, pixel 6.67, shown at step
1, values float32
Opened 7os1 map 20 as #7, grid size 32,32,40, pixel 6.67, shown at step 1,
values float32
Log from Wed Oct 1 15:41:12 2025 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 7OS1
7os1 title:
Cryo-EM structure of Brr2 in complex with Fbp21 [more info...]
Chain information for 7os1 #1
---
Chain | Description | UniProt
B | U5 small nuclear ribonucleoprotein 200 kDa helicase | U520_HUMAN 395-2129
F | WW domain-binding protein 4 | WBP4_HUMAN 198-376
> open 8d7z
8d7z title:
Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 [more info...]
Chain information for 8d7z #2
---
Chain | Description | UniProt
A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140
B | Protein cereblon | CRBN_HUMAN 1-442
C | DNA-binding protein Ikaros | IKZF1_HUMAN 112-196
Non-standard residues in 8d7z #2
---
QFC — Mezigdomide
ZN — zinc ion
> hide #!1 models
Drag select of 7 residues
> select up
197 atoms, 201 bonds, 25 residues, 1 model selected
> delete sel
Drag select of 91 residues
Drag select of 1 residues
> select clear
Drag select of 64 residues
> select up
438 atoms, 441 bonds, 82 residues, 1 model selected
> select up
5201 atoms, 5288 bonds, 771 residues, 1 model selected
> select down
438 atoms, 441 bonds, 82 residues, 1 model selected
> select clear
Drag select of 306 residues
> delete sel
> close #2.2
> show #!1 models
> hide #!1 models
> open
> /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_01_final_volume.mrc
Opened J1123_class_01_final_volume.mrc as #3, grid size 100,100,100, pixel
2.92, shown at level 0.0422, step 1, values float32
> open
> /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_00_final_volume.mrc
Opened J1123_class_00_final_volume.mrc as #4, grid size 100,100,100, pixel
2.92, shown at level 0.0558, step 1, values float32
> open
> /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_02_final_volume.mrc
Opened J1123_class_02_final_volume.mrc as #5, grid size 100,100,100, pixel
2.92, shown at level 0.0456, step 1, values float32
> open
> /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_03_final_volume.mrc
Opened J1123_class_03_final_volume.mrc as #6, grid size 100,100,100, pixel
2.92, shown at level 0.0546, step 1, values float32
> open
> /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_04_final_volume.mrc
Opened J1123_class_04_final_volume.mrc as #7, grid size 100,100,100, pixel
2.92, shown at level 0.0428, step 1, values float32
> hide #!2 models
> tile
5 models tiled
> surface dust #3 size 29.2
> surface dust #4 size 29.2
> surface dust #5 size 29.2
> surface dust #6 size 29.2
> surface dust #7 size 29.2
> volume #3 level 0.05418
> hide #!3 models
> volume #4 level 0.05357
> volume #5 level 0.04557
> volume #6 level 0.04763
> volume #7 level 0.1039
> hide #!4 models
> hide #!5 models
> hide #!7 models
> volume #6 level 0.2244
> volume #6 level 0.04238
> hide #!6 models
> close #5
> close #7
> close #6
> close #4
> close #3
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1119_006_volume_map (1).mrc"
Opened cryosparc_P391_J1119_006_volume_map (1).mrc as #3, grid size
400,400,400, pixel 0.731, shown at level 0.0159, step 2, values float32
> show #!2 models
> hide #!2 models
> volume #3 step 1
> volume #3 level 0.03852
> show #!2 models
> select add #2
9342 atoms, 9526 bonds, 4 pseudobonds, 1211 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,6.7476,0,1,0,108.36,0,0,1,-22.1
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.9497,0.11121,-0.29275,275.19,0.093635,0.99289,0.073432,89.183,0.29884,0.042326,-0.95337,148.15
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.9497,0.11121,-0.29275,273.09,0.093635,0.99289,0.073432,-1.5292,0.29884,0.042326,-0.95337,187.79
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.9497,0.11121,-0.29275,287.69,0.093635,0.99289,0.073432,-2.0098,0.29884,0.042326,-0.95337,182.62
> fitmap #2 inMap #3
Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3)
using 9342 atoms
average map value = 0.04026, steps = 124
shifted from previous position = 3.47
rotated from previous position = 11.4 degrees
atoms outside contour = 5239, contour level = 0.03852
Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc
(#3) coordinates:
Matrix rotation and translation
-0.95787247 -0.03864922 -0.28458139 308.30186913
-0.08594556 0.98406832 0.15563705 9.61657894
0.27403228 0.17353895 -0.94593369 166.53499515
Axis 0.03191650 -0.99592723 -0.08432251
Axis point 142.42454596 0.00000000 105.04054862
Rotation angle (degrees) 163.71299329
Shift along axis -13.78014654
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.99729,-0.0097977,-0.07291,286.65,-0.0036854,0.9965,-0.083501,23.711,0.073473,-0.083006,-0.99384,229.02
> ui mousemode right translate
> volume #3 level 0.01737
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.99476,0.023476,-0.099488,285.14,0.001435,0.97638,0.21605,-7.2578,0.10221,0.21477,-0.9713,186.28
> fitmap #2 inMap #3
Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3)
using 9342 atoms
average map value = 0.04026, steps = 132
shifted from previous position = 1.79
rotated from previous position = 11.7 degrees
atoms outside contour = 2693, contour level = 0.017368
Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc
(#3) coordinates:
Matrix rotation and translation
-0.95791826 -0.03877668 -0.28440985 308.30181643
-0.08600393 0.98408520 0.15549804 9.63216933
0.27385383 0.17341478 -0.94600813 166.58249595
Axis 0.03196311 -0.99593166 -0.08425250
Axis point 142.42933789 0.00000000 105.04932851
Rotation angle (degrees) 163.72355585
Shift along axis -13.77368768
> fitmap #2 inMap #3
Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3)
using 9342 atoms
average map value = 0.04026, steps = 44
shifted from previous position = 0.0119
rotated from previous position = 0.0153 degrees
atoms outside contour = 2693, contour level = 0.017368
Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc
(#3) coordinates:
Matrix rotation and translation
-0.95788952 -0.03875907 -0.28450904 308.30854641
-0.08607154 0.98404269 0.15572950 9.61715719
0.27393311 0.17365979 -0.94594023 166.54413567
Axis 0.03197672 -0.99592072 -0.08437664
Axis point 142.43117293 0.00000000 105.03855146
Rotation angle (degrees) 163.71802371
Shift along axis -13.77166550
> fitmap #2 inMap #3
Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3)
using 9342 atoms
average map value = 0.04026, steps = 44
shifted from previous position = 0.0117
rotated from previous position = 0.00577 degrees
atoms outside contour = 2695, contour level = 0.017368
Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc
(#3) coordinates:
Matrix rotation and translation
-0.95791248 -0.03880891 -0.28442493 308.30559032
-0.08610228 0.98404251 0.15571360 9.62558690
0.27384315 0.17364963 -0.94596815 166.54919827
Axis 0.03199694 -0.99592072 -0.08436887
Axis point 142.43342255 0.00000000 105.03337294
Rotation angle (degrees) 163.72324049
Shift along axis -13.77305300
> select subtract #2
Nothing selected
> ui mousemode right translate
> volume #3 level 0.03474
> show #!1 models
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.76275,-0.33241,0.55471,210.58,0.54034,0.14368,0.82909,-85.862,-0.3553,0.93212,0.070024,64.667
> view matrix models
> #1,-0.64861,-0.3233,0.68904,173.27,0.67287,0.17957,0.71764,-92.767,-0.35574,0.9291,0.10107,60.513
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.64861,-0.3233,0.68904,174.58,0.67287,0.17957,0.71764,-102.41,-0.35574,0.9291,0.10107,105.2
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.42681,-0.15092,0.89166,90.223,0.70947,0.55553,0.43363,-115.28,-0.56079,0.81769,-0.13003,183.33
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.42681,-0.15092,0.89166,87.219,0.70947,0.55553,0.43363,-104.36,-0.56079,0.81769,-0.13003,189.02
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.42681,-0.15092,0.89166,77.841,0.70947,0.55553,0.43363,-107.39,-0.56079,0.81769,-0.13003,192.33
> ui mousemode right translate
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.4752,-0.17501,0.8623,92.242,0.66584,0.56913,0.48244,-110.29,-0.57519,0.80341,-0.15392,199.81
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.4752,-0.17501,0.8623,79.426,0.66584,0.56913,0.48244,-122.16,-0.57519,0.80341,-0.15392,200.01
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.4752,-0.17501,0.8623,75.342,0.66584,0.56913,0.48244,-111.02,-0.57519,0.80341,-0.15392,195.68
> ui mousemode right translate
> select subtract #1
Nothing selected
Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.
> hide #!2 models
> fitmap #1 inMap #3
Fit molecule 7os1 (#1) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3)
using 14054 atoms
average map value = 0.008903, steps = 2000
shifted from previous position = 7.69
rotated from previous position = 22.3 degrees
atoms outside contour = 12497, contour level = 0.034742
Position of 7os1 (#1) relative to cryosparc_P391_J1119_006_volume_map (1).mrc
(#3) coordinates:
Matrix rotation and translation
-0.62261579 -0.16535463 0.76485778 112.64603008
0.37840411 0.79192285 0.47923744 -106.36242327
-0.68495249 0.58780613 -0.43049280 277.53222150
Axis 0.06994379 0.93401912 0.35030864
Axis point 130.50602909 0.00000000 130.11272413
Rotation angle (degrees) 129.09387669
Shift along axis 5.75628873
> show #!2 models
> hide #!3 models
> hide #!2 models
> color #!1 bychain
> rainbow #!1
> show #!2 models
> open
> /Users/zrizvi/Downloads/fold_2025_10_01_14_30/fold_2025_10_01_14_30_model_0.cif
Chain information for fold_2025_10_01_14_30_model_0.cif #4
---
Chain | Description
A | .
B | .
C | .
> mmaker #4 to #2
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 8d7z, chain A (#2) with fold_2025_10_01_14_30_model_0.cif, chain A
(#4), sequence alignment score = 5128.5
RMSD between 782 pruned atom pairs is 0.703 angstroms; (across all 826 pairs:
1.841)
> hide #!1 models
> hide #!2 models
Drag select of 201 residues
> select up
1708 atoms, 1736 bonds, 219 residues, 1 model selected
> select up
26102 atoms, 26594 bonds, 3276 residues, 1 model selected
> select down
1708 atoms, 1736 bonds, 219 residues, 1 model selected
> select clear
Drag select of 351 residues
> delete sel
Drag select of 19 residues
> select up
408 atoms, 413 bonds, 53 residues, 1 model selected
> delete sle
Missing or invalid "atoms" argument: invalid atoms specifier
> delete sel
> color #!4 bychain
> show #!2 models
> show #!1 models
> hide #!2 models
> hide #!1 models
> ui tool show "Show Sequence Viewer"
[Repeated 1 time(s)]
> sequence chain #4/C
Alignment identifier is 4/C
> select #4/C:35
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/C:35-43
65 atoms, 65 bonds, 9 residues, 1 model selected
> select #4/C:93
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #4/C:93-289
1568 atoms, 1585 bonds, 197 residues, 1 model selected
> select #4/C:2136
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #4/C:1897-2136
1894 atoms, 1927 bonds, 240 residues, 1 model selected
> select clear
> select #4/a
6475 atoms, 6591 bonds, 2 pseudobonds, 824 residues, 2 models selected
> delete sel
> select #4/b
3135 atoms, 3209 bonds, 389 residues, 1 model selected
> select #4/b
3135 atoms, 3209 bonds, 389 residues, 1 model selected
> delete sel
> mmaker #4 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 7os1, chain B (#1) with fold_2025_10_01_14_30_model_0.cif, chain C
(#4), sequence alignment score = 8690
RMSD between 1278 pruned atom pairs is 1.099 angstroms; (across all 1720
pairs: 2.058)
> show #!1 models
> select clear
> select #4/C:35-155
971 atoms, 978 bonds, 1 pseudobond, 120 residues, 2 models selected
> select clear
Drag select of 435 residues
> show #!2 models
> hide #!4 models
> select add #4
18614 atoms, 17227 bonds, 1 pseudobond, 2318 residues, 3 models selected
> select subtract #4
1711 atoms, 217 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,-0.62262,-0.16535,0.76486,115.18,0.3784,0.79192,0.47924,-109.02,-0.68495,0.58781,-0.43049,289.31
> ui mousemode right translate
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> select add #2
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected
> combine sel
Remapping chain ID 'B' in 8d7z #2 to 'D'
> select subtract #2
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> hide #!2 models
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected
> select subtract #5
Nothing selected
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected
> select subtract #5
Nothing selected
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected
> select clear
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected
> molmap map sel 20
Missing or invalid "atoms" argument: invalid atoms specifier
> molmap sel 20
Opened combination map 20 as #6, grid size 41,40,47, pixel 6.67, shown at
level 0.0439, step 1, values float32
> volume #6 style image
> select subtract #5
Nothing selected
> hide #!5 models
> color #6 #d6d6d6ff models
> volume #6 level 0,0 level 0.2577,0.8 level 0.5978,1
> volume #6 level 0,0 level 0.2181,0.9176 level 0.5978,1
> hide #!6 models
> show #!1 models
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> molmap sel 20
Opened 7os1 map 20 as #7, grid size 32,32,40, pixel 6.67, shown at level
0.042, step 1, values float32
> volume #7 style image maximumIntensityProjection true
> volume #7 maximumIntensityProjection false
> select subtract #1
Nothing selected
> hide #!1 models
> color #7 darkgrey models
> volume #7 level 0,0 level 0.263,0.8 level 0.3416,1
> volume #7 level 0,0 level 0.2195,0.9559 level 0.3416,1
> volume #6 level 0,0 level 0.2137,0.9176 level 0.5978,1
> volume #7 level 0,0 level 0.2353,0.9853 level 0.3416,1
> show #!1 models
> hide #!7 models
Drag select of 248 residues
> ui tool show "Show Sequence Viewer"
> sequence chain #1/B
Alignment identifier is 1/B
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo
> lab/alphafold and cryo structures .cxs" includeMaps true
——— End of log from Wed Oct 1 15:41:12 2025 ———
> view name session-start
opened ChimeraX session
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> select subtract #1
Nothing selected
> hide #!1 models
> show #!1 models
> show #!2 models
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1144_010_volume_map (3).mrc"
Opened cryosparc_P391_J1144_010_volume_map (3).mrc as #8, grid size
500,500,500, pixel 0.731, shown at level 0.00574, step 2, values float32
> ~tile
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right translate
> hide #!2 models
> show #!2 models
> hide #!1 models
> select subtract #1
Nothing selected
> select add #2
9342 atoms, 9526 bonds, 4 pseudobonds, 1211 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
9342 atoms, 9526 bonds, 4 pseudobonds, 1211 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.62262,-0.16535,0.76486,81.218,0.3784,0.79192,0.47924,35.418,-0.68495,0.58781,-0.43049,356.36
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.52947,-0.46913,-0.70681,131.84,-0.0018161,0.83255,-0.55395,192.27,0.84832,0.29459,0.43996,100.47
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.52947,-0.46913,-0.70681,163.98,-0.0018161,0.83255,-0.55395,99.716,0.84832,0.29459,0.43996,60.267
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.52947,-0.46913,-0.70681,153.85,-0.0018161,0.83255,-0.55395,115.19,0.84832,0.29459,0.43996,14.033
> ui mousemode right translate
> fitmap #2 inMap #8
Fit molecule 8d7z (#2) to map cryosparc_P391_J1144_010_volume_map (3).mrc (#8)
using 9342 atoms
average map value = 0.02757, steps = 604
shifted from previous position = 8.82
rotated from previous position = 35.9 degrees
atoms outside contour = 2104, contour level = 0.0057392
Position of 8d7z (#2) relative to cryosparc_P391_J1144_010_volume_map (3).mrc
(#8) coordinates:
Matrix rotation and translation
-0.94498524 -0.13700654 -0.29703890 358.50627603
-0.15015795 0.98842154 0.02180467 62.42466926
0.29061226 0.06520784 -0.95461639 195.04032059
Axis 0.07363977 -0.99703526 -0.02231328
Axis point 166.88663288 0.00000000 124.13833462
Rotation angle (degrees) 162.86049384
Shift along axis -40.19126691
> volume #8 step 1
> volume #8 level 0.0185
> select subtract #2
Nothing selected
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> show #!1 models
> select subtract #1
Nothing selected
> hide #!8 models
> show #!8 models
> hide #!2 models
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.78755,-0.062423,-0.61309,107.31,-0.49475,-0.65719,-0.56862,362.63,-0.36742,0.75113,-0.54845,240.32
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.78755,-0.062423,-0.61309,153.92,-0.49475,-0.65719,-0.56862,461.83,-0.36742,0.75113,-0.54845,237.4
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.82415,-0.46278,-0.32651,159.31,-0.55854,-0.56858,-0.60395,464.32,0.093848,0.68012,-0.72707,208.27
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.41398,-0.8695,-0.26942,262.77,-0.71075,-0.12384,-0.69246,439.9,0.56873,0.47815,-0.66927,159.44
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.41398,-0.8695,-0.26942,253.58,-0.71075,-0.12384,-0.69246,438.33,0.56873,0.47815,-0.66927,166.04
> ui mousemode right zoom
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #1,-0.041288,0.98751,0.15205,8.4958,0.88517,0.10674,-0.45287,146.71,-0.46344,0.11589,-0.87852,391.04
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.10446,0.99297,0.055625,1.5307,0.78977,-0.048827,-0.61146,204.43,-0.60444,0.1078,-0.78932,398.76
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.10446,0.99297,0.055625,-5.241,0.78977,-0.048827,-0.61146,195.76,-0.60444,0.1078,-0.78932,394.65
> select subtract #1
Nothing selected
> show #!2 models
> hide #!8 models
> show #!8 models
> show #!4 models
> hide #!2 models
> hide #!1 models
> hide #!8 models
> hide #!4 models
> show #!5 models
> show #!8 models
> hide #!8 models
> hide #!5 models
> show #!6 models
> hide #!6 models
> show #!7 models
> hide #!7 models
> show #!8 models
> show #!4 models
> hide #!4 models
> show #!5 models
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected
> view matrix models
> #5,-0.62262,-0.16535,0.76486,84.031,0.3784,0.79192,0.47924,-27.256,-0.68495,0.58781,-0.43049,397.84
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.23307,-0.039665,-0.97165,220.35,-0.92806,0.2894,-0.23442,371.82,0.29049,0.95639,0.030638,112.82
> view matrix models
> #5,-0.25444,0.32243,-0.91176,254.57,-0.59917,0.68749,0.41032,162.86,0.75912,0.6507,0.018267,67.658
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.25444,0.32243,-0.91176,288.43,-0.59917,0.68749,0.41032,124.14,0.75912,0.6507,0.018267,-7.2692
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.205,0.26166,-0.94314,291.85,-0.40157,0.85628,0.32485,86.787,0.89259,0.44533,-0.070459,7.112
> fitmap #5 inMap #8
Fit molecule combination (#5) to map cryosparc_P391_J1144_010_volume_map
(3).mrc (#8) using 23396 atoms
average map value = 0.01806, steps = 224
shifted from previous position = 3.14
rotated from previous position = 4.36 degrees
atoms outside contour = 14277, contour level = 0.018501
Position of combination (#5) relative to cryosparc_P391_J1144_010_volume_map
(3).mrc (#8) coordinates:
Matrix rotation and translation
-0.64099015 -0.20317454 0.74017007 166.33811566
0.23370661 0.86687742 0.44034618 -48.45752700
-0.73110385 0.45524020 -0.50817666 342.92513809
Axis 0.00970396 0.95858454 0.28464279
Axis point 163.39250809 0.00000000 138.21080909
Rotation angle (degrees) 129.87722940
Shift along axis 52.77467107
> ui mousemode right translate
> select subtract #5
Nothing selected
> show #!1 models
> show #!2 models
> hide #!8 models
> hide #!5 models
> show #!5 models
> hide #!1 models
> hide #!2 models
> hide #!5 models
> show #!1 models
> show #!2 models
> show #!8 models
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> fitmap #1 inMap #8
Fit molecule 7os1 (#1) to map cryosparc_P391_J1144_010_volume_map (3).mrc (#8)
using 14054 atoms
average map value = 0.01454, steps = 296
shifted from previous position = 19.8
rotated from previous position = 17 degrees
atoms outside contour = 9546, contour level = 0.018501
Position of 7os1 (#1) relative to cryosparc_P391_J1144_010_volume_map (3).mrc
(#8) coordinates:
Matrix rotation and translation
0.71641153 -0.50828522 0.47791281 64.65020261
0.40829833 -0.25000248 -0.87794717 316.84320098
0.56572696 0.82410248 0.02842735 12.66524064
Axis 0.87954354 -0.04537845 0.47364961
Axis point 0.00000000 164.61195793 129.02594166
Rotation angle (degrees) 104.63034271
Shift along axis 48.48370216
> select subtract #1
Nothing selected
> hide #!8 models
> show #!8 models
> close #5
> close #6
> select add #1
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> select add #2
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected
> combine sel
Remapping chain ID 'B' in 8d7z #2 to 'D'
> select subtract #2
14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected
> hide #!1 models
> hide #!2 models
> select subtract #1
Nothing selected
> rename #5 "combination of 8d7z and 7os1"
> hide #!8 models
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected
> select subtract #5
Nothing selected
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected
> molmap map sel 15
Missing or invalid "atoms" argument: invalid atoms specifier
> molmap sel 15
Opened combination of 8d7z and 7os1 map 15 as #6, grid size 46,48,51, pixel 5,
shown at level 0.0562, step 1, values float32
> vop resample #6 ongrid #8
Opened combination of 8d7z and 7os1 map 15 resampled as #9, grid size
500,500,500, pixel 0.731, shown at step 1, values float32
> save snrnp fullmask.mrc #9
Cannot determine format for 'snrnp'
> save snrnp_fullmask.mrc #9
> hide #!9 models
> select subtract #5
Nothing selected
> split #5
Split combination of 8d7z and 7os1 (#5) into 5 models
Chain information for combination of 8d7z and 7os1 A #5.1
---
Chain | Description
A | No description available
Chain information for combination of 8d7z and 7os1 B #5.2
---
Chain | Description
B | No description available
Chain information for combination of 8d7z and 7os1 D #5.4
---
Chain | Description
D | No description available
Chain information for combination of 8d7z and 7os1 F #5.5
---
Chain | Description
F | No description available
> select add #5.1
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select add #5.2
20184 atoms, 20590 bonds, 2546 residues, 2 models selected
> select add #5.3
20189 atoms, 20593 bonds, 2548 residues, 3 models selected
> select add #5.4
23176 atoms, 23653 bonds, 4 pseudobonds, 2931 residues, 5 models selected
> select subtract #5.4
20189 atoms, 20593 bonds, 2548 residues, 3 models selected
> select subtract #5.3
20184 atoms, 20590 bonds, 2546 residues, 2 models selected
> select subtract #5.1
13834 atoms, 14127 bonds, 1720 residues, 1 model selected
> select add #5.4
16821 atoms, 17187 bonds, 4 pseudobonds, 2103 residues, 3 models selected
> combine sel
> select subtract #5.2
2987 atoms, 3060 bonds, 4 pseudobonds, 383 residues, 2 models selected
> select add #5.3
2992 atoms, 3063 bonds, 4 pseudobonds, 385 residues, 3 models selected
> select subtract #5.3
2987 atoms, 3060 bonds, 4 pseudobonds, 383 residues, 2 models selected
> select subtract #5.4
Nothing selected
> hide #!5 models
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> select add #10
16821 atoms, 17187 bonds, 4 pseudobonds, 2103 residues, 2 models selected
> molmap sel 15
Opened combination map 15 as #11, grid size 39,43,47, pixel 5, shown at level
0.0543, step 1, values float32
> vop resample #11 ongrid #8
Opened combination map 15 resampled as #12, grid size 500,500,500, pixel
0.731, shown at step 1, values float32
> save snrnp_halfmask.mrc #12
> show #!9 models
> select subtract #10
Nothing selected
> hide #!10 models
> hide #!12 models
> hide #!9 models
> show #!12 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo
> lab/alphafold and cryo structures .cxs" includeMaps true
——— End of log from Tue Oct 28 15:23:27 2025 ———
> view name session-start
opened ChimeraX session
> hide #!12 models
> show #!3 models
> hide #!3 models
> show #!4 models
> hide #!4 models
> show #!5 models
> show #!8 models
> show #!9 models
> hide #!9 models
> show #!10 models
> hide #!10 models
> show #!11 models
> hide #!11 models
> show #!12 models
> hide #!12 models
> hide #!8 models
> show #!10 models
> hide #!10 models
> show #!9 models
> hide #!9 models
> show #!6 models
> hide #!6 models
> hide #!5 models
> show #!5 models
> select add #5.1
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select add #5.2
20184 atoms, 20590 bonds, 2546 residues, 2 models selected
> select subtract #5.2
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select add #5.3
6355 atoms, 6466 bonds, 828 residues, 2 models selected
> select subtract #5.3
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select add #5.4
9337 atoms, 9523 bonds, 4 pseudobonds, 1209 residues, 3 models selected
> select subtract #5.4
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select add #5.4
9337 atoms, 9523 bonds, 4 pseudobonds, 1209 residues, 3 models selected
> select subtract #5.4
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> color #5.1 darkgrey
> select add #5.4
9337 atoms, 9523 bonds, 4 pseudobonds, 1209 residues, 3 models selected
> select subtract #5.1
2987 atoms, 3060 bonds, 4 pseudobonds, 383 residues, 2 models selected
> color #5.4 #ff8ad8ff
> select subtract #5.4
Nothing selected
> set bgColor white
> set bgColor #ffffff00
> graphics silhouettes true
> lighting shadows true
> lighting soft
Cell requested for row 9 is out of bounds for table with 17 rows! Resizing
table model.
> hide #!5.4 models
> hide #5.1 models
> show #5.1 models
> ui tool show "Show Sequence Viewer"
> select add #5.1
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select subtract #5.1
Nothing selected
> select add #5.1
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select subtract #5.1
Nothing selected
> select add #5.2
13834 atoms, 14127 bonds, 1720 residues, 1 model selected
> select subtract #5.2
Nothing selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5.2/B
Alignment identifier is 5.2/B
> select #5.2/B:635
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #5.2/B:635-1014
3032 atoms, 3087 bonds, 380 residues, 1 model selected
> select #5.2/B:406
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #5.2/B:406-456
417 atoms, 427 bonds, 51 residues, 1 model selected
> select
> #5.2/B:410-415,418-422,463-473,482-494,508-523,532-536,544-563,572-583,589-599,616-643,657-665,677-681,696-715,729-745,748-754,760-767,773-778,790-803,813-819,845-856,875-884,892-908,912-920,923-932,939-946,949-967,982-991,994-1005,1010-1025,1030-1042,1054-1069,1074-1102,1104-1121,1127-1132,1136-1146,1151-1179,1308-1312,1314-1322,1329-1342,1355-1371,1382-1402,1411-1422,1428-1438,1442-1447,1456-1461,1464-1482,1496-1505,1515-1519,1534-1554,1565-1583,1593-1604,1606-1614,1625-1638,1649-1651,1680-1689,1710-1719,1732-1742,1747-1756,1758-1764,1767-1772,1777-1799,1813-1822,1825-1836,1841-1856,1863-1875,1886-1900,1905-1934,1936-1952,1958-1963,1967-1978,1981-1987,1989-1997,2000-2014
7408 atoms, 7457 bonds, 917 residues, 1 model selected
> select clear
Drag select of 32 residues
> select add #5.1
6620 atoms, 6463 bonds, 858 residues, 2 models selected
> show #!5.4 models
> select add #5.2
20184 atoms, 20590 bonds, 2546 residues, 2 models selected
> select subtract #5.2
6350 atoms, 6463 bonds, 826 residues, 1 model selected
> select subtract #5.1
Nothing selected
> select add #5.2
13834 atoms, 14127 bonds, 1720 residues, 1 model selected
> select subtract #5.2
Nothing selected
> show #!4 models
> hide #!5 models
> mmaker #4 to #5.2
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 combination of 8d7z and 7os1 B, chain B (#5.2) with
fold_2025_10_01_14_30_model_0.cif, chain C (#4), sequence alignment score =
8641.7
RMSD between 1278 pruned atom pairs is 1.099 angstroms; (across all 1720
pairs: 2.058)
> show #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!5.4 models
> hide #5.1 models
> show #5.1 models
> hide #!5 models
> ui tool show "Show Sequence Viewer"
> sequence chain #4/C
Destroying pre-existing alignment with identifier 4/C
Alignment identifier is 4/C
Drag select of 24 residues
> show #!5 models
> show #!5.4 models
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1237_008_volume_map (1).mrc"
Opened cryosparc_P391_J1237_008_volume_map (1).mrc as #13, grid size
500,500,500, pixel 0.731, shown at level 0.00814, step 2, values float32
> open "/Users/zrizvi/Downloads/cryosparc_P391_J1238_010_volume_map (1).mrc"
Opened cryosparc_P391_J1238_010_volume_map (1).mrc as #14, grid size
500,500,500, pixel 0.731, shown at level 0.00594, step 2, values float32
> volume #13 step 1
> volume #14 step 1
> volume #13 level 0.01572
> volume #14 level 0.02668
> hide #!14 models
> select add #13
198 atoms, 24 residues, 3 models selected
> select clear
> hide #!13 models
> hide #!4 models
> show #!13 models
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> select add #13
2 models selected
> view matrix models
> #13,-0.40708,0.64359,0.64813,21.263,0.76667,-0.14495,0.62547,-26.92,0.49649,0.75152,-0.43442,11.391
> volume #13 level 0.02141
> select subtract #13
Nothing selected
> ui mousemode right "translate selected models"
> select add #13
2 models selected
> view matrix models
> #13,-0.40708,0.64359,0.64813,-31.181,0.76667,-0.14495,0.62547,-2.5381,0.49649,0.75152,-0.43442,181.75
> view matrix models
> #13,-0.41621,-0.14575,0.89751,82.455,0.87303,0.21182,0.43925,-60.274,-0.25413,0.96638,0.039083,197.78
> view matrix models
> #13,-0.41621,-0.14575,0.89751,82.358,0.87303,0.21182,0.43925,-117.18,-0.25413,0.96638,0.039083,81.064
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #13,-0.41621,-0.14575,0.89751,60.201,0.87303,0.21182,0.43925,-86.461,-0.25413,0.96638,0.039083,66.029
> ui mousemode right translate
> show #!6 models
> hide #!5 models
> hide #!6 models
> show #!5 models
> select add #5
23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 10 models selected
> combine sel
> hide #!5 models
> select subtract #5
2 models selected
> fitmap #15 inMap #13
Fit molecule combination (#15) to map cryosparc_P391_J1237_008_volume_map
(1).mrc (#13) using 23396 atoms
average map value = 0.01863, steps = 160
shifted from previous position = 7.09
rotated from previous position = 8.2 degrees
atoms outside contour = 14763, contour level = 0.021405
Position of combination (#15) relative to cryosparc_P391_J1237_008_volume_map
(1).mrc (#13) coordinates:
Matrix rotation and translation
0.90723292 -0.41836122 -0.04361567 126.05050383
-0.17516036 -0.28148482 -0.94344324 397.35514291
0.38242291 0.86356250 -0.32865259 87.87025567
Axis 0.96506864 -0.22753468 0.12988643
Axis point 0.00000000 183.98793041 181.54924620
Rotation angle (degrees) 110.57616654
Shift along axis 42.64846573
> select clear
> volume #13 level 0.02899
> fitmap #15 inMap #13
Fit molecule combination (#15) to map cryosparc_P391_J1237_008_volume_map
(1).mrc (#13) using 23396 atoms
average map value = 0.01863, steps = 60
shifted from previous position = 0.0153
rotated from previous position = 0.0178 degrees
atoms outside contour = 16676, contour level = 0.028988
Position of combination (#15) relative to cryosparc_P391_J1237_008_volume_map
(1).mrc (#13) coordinates:
Matrix rotation and translation
0.90720498 -0.41845121 -0.04333255 126.00945335
-0.17497904 -0.28165974 -0.94342468 397.34395821
0.38257216 0.86346186 -0.32874331 87.88937865
Axis 0.96506180 -0.22747658 0.13003898
Axis point 0.00000000 183.97407112 181.52330203
Rotation angle (degrees) 110.58515031
Shift along axis 42.64951029
> color #13 darkgrey models
> graphics silhouettes false
> lighting shadows true intensity 0.5
> lighting soft
> graphics silhouettes true
> color #13 #a9a9a996 models
> show #!14 models
> show #!12 models
> hide #!12 models
> hide #!13 models
> show #!13 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> select add #14
2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #14,-0.27306,0.17368,0.94619,-4.7228,0.95941,0.12132,0.2546,-44.149,-0.070576,0.9773,-0.19976,61.475
> ui mousemode right "translate selected models"
> view matrix models
> #14,-0.27306,0.17368,0.94619,-54.719,0.95941,0.12132,0.2546,-67.195,-0.070576,0.9773,-0.19976,66.438
> ui mousemode right translate
> select subtract #14
Nothing selected
> hide #!14 models
> volume #13 level 0.01509
> show #!14 models
> select add #14
2 models selected
> vop flip #14
Opened cryosparc_P391_J1238_010_volume_map (1).mrc z flip as #16, grid size
500,500,500, pixel 0.731, shown at step 1, values float32
> select subtract #14
Nothing selected
> select add #16
2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.33284,-0.26172,0.90594,39.593,0.44786,0.80157,0.39611,-131.94,-0.82985,0.53757,-0.14958,257.12
> view matrix models
> #16,-0.39732,-0.27458,0.87564,57.562,0.50217,0.73359,0.45789,-139.47,-0.76809,0.62165,-0.15358,232.98
> select subtract #16
Nothing selected
> hide #!13 models
> show #!13 models
> show #!15 models
> hide #!15 models
> ui mousemode right translate
> hide #!16 models
> show #!16 models
> ui mousemode right "rotate selected models"
> select add #16
2 models selected
> view matrix models
> #16,0.10865,0.049021,-0.99287,251.16,0.71835,-0.69427,0.044327,154.05,-0.68715,-0.71804,-0.11064,451.25
> view matrix models
> #16,0.10865,0.049021,-0.99287,246.14,0.71835,-0.69427,0.044327,164.76,-0.68715,-0.71804,-0.11064,485.85
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #16,-0.39734,-0.011001,-0.9176,324.24,0.71547,-0.62987,-0.30226,215.34,-0.57465,-0.77662,0.25815,412.8
> view matrix models
> #16,-0.39734,-0.011001,-0.9176,332.46,0.71547,-0.62987,-0.30226,227.31,-0.57465,-0.77662,0.25815,406.72
> ui mousemode right translate
> fitmap #16 inMap #13
Fit map cryosparc_P391_J1238_010_volume_map (1).mrc z flip in map
cryosparc_P391_J1237_008_volume_map (1).mrc using 576297 points
correlation = 0.6701, correlation about mean = 0.1934, overlap = 1306
steps = 156, shift = 16, angle = 7.69 degrees
Position of cryosparc_P391_J1238_010_volume_map (1).mrc z flip (#16) relative
to cryosparc_P391_J1237_008_volume_map (1).mrc (#13) coordinates:
Matrix rotation and translation
0.94125601 -0.33768525 -0.00240969 72.29113111
-0.33024548 -0.92196215 0.20229613 368.64395968
-0.07053407 -0.18961666 -0.97932143 382.05012944
Axis -0.98505407 0.17122735 0.01869949
Axis point 0.00000000 210.08914741 172.90339257
Rotation angle (degrees) 168.52562910
Shift along axis -0.94460007
> select clear
> hide #!13 models
> show #!13 models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo
> lab/alphafold and cryo structures-IMPO .cxs" includeMaps true
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!13 models
> color #16 #b2b2ffc6 models
> color #16 #b2b2ffc7 models
> show #!13 models
> hide #!15 models
> hide #!16 models
> show #!16 models
> show #!15 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> volume #13 level 0.02014
> movie record
> turn y 2 180
> wait 180
> movie encode /Users/zrizvi/Desktop/movie5.mp4
Movie saved to /Users/zrizvi/Desktop/movie5.mp4
> oepn EMD:13045
Unknown command: oepn EMD:13045
> oepn EMDB:13045
Unknown command: oepn EMDB:13045
> oepn EMDB13045
Unknown command: oepn EMDB13045
> oepn EMDB-13045
Unknown command: oepn EMDB-13045
> oepn EMDB:13045
Unknown command: oepn EMDB:13045
> open EMDB:13045
Opened emdb 13045 as #17, grid size 336,336,336, pixel 0.832, shown at level
0.3, step 2, values float32, fit PDB 7os1
> hide #!15 models
> hide #!13 models
> show #!13 models
> show #!15 models
> hide #!13 models
> select add #17
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #17,1,0,0,9.4039,0,1,0,54.781,0,0,1,92.25
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.20156,0.90274,-0.38004,115.82,0.94344,0.074664,-0.32302,91.706,-0.26322,-0.42366,-0.86673,461.35
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.20156,0.90274,-0.38004,114.96,0.94344,0.074664,-0.32302,110.81,-0.26322,-0.42366,-0.86673,428.1
> ui mousemode right translate
> ui mousemode right "rotate selected models"
> view matrix models
> #17,-0.22962,0.94469,-0.23416,91.821,0.85556,0.081231,-0.51128,150.18,-0.46399,-0.31774,-0.8269,436.59
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.22962,0.94469,-0.23416,84.856,0.85556,0.081231,-0.51128,153.26,-0.46399,-0.31774,-0.8269,449.23
> ui mousemode right translate
> select add #5.1
6350 atoms, 6463 bonds, 826 residues, 3 models selected
> select subtract #5.1
2 models selected
> select subtract #17
Nothing selected
> hide #!15 models
> show #!5 models
> hide #!5.5 models
> hide #!5.4 models
> hide #5.1 models
> hide #5.2 models
> show #5.2 models
> hide #5.3 models
> show #5.3 models
> hide #5.3 models
> show #!15 models
> mmaker #5.2 to #15
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 combination, chain B (#15) with combination of 8d7z and 7os1 B,
chain B (#5.2), sequence alignment score = 8944.7
RMSD between 1720 pruned atom pairs is 0.000 angstroms; (across all 1720
pairs: 0.000)
> hide #!15 models
> select add #17
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #17,-0.22962,0.94469,-0.23416,84.537,0.85556,0.081231,-0.51128,152.65,-0.46399,-0.31774,-0.8269,448.64
> ui mousemode right "rotate selected models"
> view matrix models
> #17,0.16974,0.98005,-0.10336,3.9864,0.81406,-0.19855,-0.54579,200.75,-0.55542,0.0085042,-0.83152,418.96
> ui mousemode right "translate selected models"
> view matrix models
> #17,0.16974,0.98005,-0.10336,0.11539,0.81406,-0.19855,-0.54579,200.21,-0.55542,0.0085042,-0.83152,421.5
Must specify one map, got 0
> fitmap #5.2 inMap #17
Fit molecule combination of 8d7z and 7os1 B (#5.2) to map emdb 13045 (#17)
using 13834 atoms
average map value = 0.6118, steps = 160
shifted from previous position = 9.89
rotated from previous position = 15.8 degrees
atoms outside contour = 2903, contour level = 0.3
Position of combination of 8d7z and 7os1 B (#5.2) relative to emdb 13045 (#17)
coordinates:
Matrix rotation and translation
0.99999996 -0.00006778 0.00028701 -0.02237487
0.00006789 0.99999993 -0.00037564 0.02489738
-0.00028698 0.00037566 0.99999989 -0.01357518
Axis 0.78657896 0.60093128 0.14203919
Axis point 0.00000000 34.43194076 73.57719080
Rotation angle (degrees) 0.02736328
Shift along axis -0.00456619
> select clear
> show #!15 models
> mmaker #15 to #5.2
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 combination of 8d7z and 7os1 B, chain B (#5.2) with combination,
chain B (#15), sequence alignment score = 8944.7
RMSD between 1720 pruned atom pairs is 0.000 angstroms; (across all 1720
pairs: 0.000)
> hide #5.2 models
> color #17 #ffb2b2a3 models
> show #!14 models
> hide #!14 models
> show #!13 models
> hide #!15 models
> color #17 #ffb2b2ff models
> save "/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo
> lab/alphafold and cryo structures-IMPO .cxs" includeMaps true
——— End of log from Mon Nov 24 16:39:31 2025 ———
> view name session-start
opened ChimeraX session
OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
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: Mac16,1
Model Number: MW2V3LL/A
Chip: Apple M4
Total Number of Cores: 10 (4 performance and 6 efficiency)
Memory: 16 GB
System Firmware Version: 11881.140.96
OS Loader Version: 11881.140.96
Software:
System Software Overview:
System Version: macOS 15.6.1 (24G90)
Kernel Version: Darwin 24.6.0
Time since boot: 3 days, 20 hours, 29 minutes
Graphics/Displays:
Apple M4:
Chipset Model: Apple M4
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
Installed Packages:
alabaster: 1.0.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.2.0
autocommand: 2.2.2
babel: 2.17.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.3
blockdiag: 3.0.0
blosc2: 3.2.0
build: 1.2.2.post1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.1
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.19.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Aniso: 1.1.1
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.60.5
ChimeraX-AtomicLibrary: 14.1.13
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.10.dev202503130118
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
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: 1.8.dev0
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.5.1
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: 2.1.7
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.15
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-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: 2.7.7
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: 1.1.2
ChimeraX-ProfileGrids: 1.0.2
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
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
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
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: 1.44
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: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
coverage: 7.6.12
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.12
debugpy: 1.8.13
decorator: 5.2.1
docutils: 0.21.2
executing: 2.2.0
filelock: 3.17.0
fonttools: 4.56.0
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.13.0
html2text: 2024.2.26
idna: 3.10
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.0.0
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.1
Jinja2: 3.1.6
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.8
line_profiler: 4.2.0
lxml: 5.3.1
lz4: 4.4.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.1.0
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
OpenMM: 8.2.0
openvr: 1.26.701
packaging: 24.2
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: 4.3.6
platformdirs: 4.2.2
pluggy: 1.5.0
prompt_toolkit: 3.0.50
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.32
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: 3.2.1
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: 8.3.5
pytest-cov: 6.0.0
python-dateutil: 2.9.0.post0
pytz: 2025.1
pyzmq: 26.3.0
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
Send2Trash: 1.8.3
SEQCROW: 1.8.21
setuptools: 75.8.2
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
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: 2024.7.24
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4.2
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2025.1
urllib3: 2.3.0
wcwidth: 0.2.13
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.43.0
wheel-filename: 1.4.2
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 7 days 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 , 7 days ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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."
The ChimeraX release candidate and daily builds use a newer Qt version where this crash has not been reported. So you might try either of those.
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Reported by Zeba Rizvi