![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17340 closed defect (duplicate)
Crash moving window between screens
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.7.1-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff84a1b0f80 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, 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._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.dssp._dssp, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 101)
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{
"uptime" : 140000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,4",
"coalitionID" : 5103,
"osVersion" : {
"train" : "macOS 14.7.1",
"build" : "23H222",
"releaseType" : "User"
},
"captureTime" : "2025-04-09 14:46:33.2817 -0400",
"codeSigningMonitor" : 0,
"incident" : "811A797F-0360-4CD0-B828-0E2FDC168C1A",
"pid" : 96287,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-07 16:45:49.1843 -0400",
"procStartAbsTime" : 15453478964172,
"procExitAbsTime" : 149749604903743,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.8.0","CFBundleVersion":"1.8.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"FAD1F7A5-AFC8-5CA0-970D-04CC3EEAC657","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "2145464F-803C-5923-4D0A-4BF9FED76F62",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 4986,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "BCC22267-C561-4244-AF15-EF96F41B6F1C",
"sip" : "enabled",
"vmRegionInfo" : "0 is not in any region. Bytes before following region: 4430372864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108122000-108126000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
"exception" : {"codes":"0x000000000000000d, 0x0000000000000000","rawCodes":[13,0],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"UNKNOWN_0xD at 0x0000000000000000"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":96287},
"vmregioninfo" : "0 is not in any region. Bytes before following region: 4430372864\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 108122000-108126000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX",
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"faultingThread" : 0,
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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/ruchigautamsharma/Downloads/9gz1.cif
9gz1.cif title:
Beta-cardiac myosin interacting heads motif complexed to mavacamten [more
info...]
Chain information for 9gz1.cif #1
---
Chain | Description | UniProt
A B | Myosin-7 | MYH7_HUMAN 2-1138
C E | Myosin light chain 1/3, skeletal muscle isoform | MYL1_MOUSE 1-187
D F | Myosin regulatory light chain 11 | MYL11_MOUSE 1-168
Non-standard residues in 9gz1.cif #1
---
ADP — adenosine-5'-diphosphate
MG — magnesium ion
PO4 — phosphate ion
XB2 —
6-[[(1~{S})-1-phenylethyl]amino]-3-propan-2-yl-1~{H}-pyrimidine-2,4-dione
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/cryosparc_P30_J395_004_volume_map_sharp.mrc
Opened cryosparc_P30_J395_004_volume_map_sharp.mrc as #2, grid size
300,300,300, pixel 0.83, shown at level 0.0692, step 2, values float32
> select add #1
19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-0.87037,0,1,0,-36.512,0,0,1,32.991
> view matrix models #1,1,0,0,-1.4608,0,1,0,-66.48,0,0,1,62.095
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.22929,0.90551,0.35704,-80.488,-0.95278,0.13376,0.27263,167.42,0.19911,-0.40268,0.89342,110.69
> view matrix models
> #1,-0.41226,0.5412,0.7329,14.553,-0.87648,-0.45515,-0.15692,311.05,0.24865,-0.70707,0.66199,184.84
> view matrix models
> #1,-0.71467,-0.017305,0.69925,150.47,-0.54439,-0.61395,-0.57159,348.27,0.43919,-0.78916,0.42935,204.02
> view matrix models
> #1,-0.44098,0.53067,-0.72382,237.56,-0.35154,-0.84416,-0.40473,330.42,-0.8258,0.075977,0.55882,238.21
> view matrix models
> #1,0.25981,-0.28602,-0.92233,289.58,-0.39672,-0.90242,0.1681,260.71,-0.88041,0.32223,-0.34793,343.44
> view matrix models
> #1,0.88601,-0.41122,-0.21422,110.78,-0.38472,-0.90986,0.15541,261.97,-0.25882,-0.055284,-0.96434,401.68
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.88601,-0.41122,-0.21422,107.68,-0.38472,-0.90986,0.15541,291.22,-0.25882,-0.055284,-0.96434,313.09
> view matrix models
> #1,0.88601,-0.41122,-0.21422,91.725,-0.38472,-0.90986,0.15541,294.03,-0.25882,-0.055284,-0.96434,306.38
> view matrix models
> #1,0.88601,-0.41122,-0.21422,90.734,-0.38472,-0.90986,0.15541,294.35,-0.25882,-0.055284,-0.96434,306.01
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.98592,-0.10775,-0.12785,16.255,-0.09588,-0.99079,0.095617,273.05,-0.13697,-0.082013,-0.98717,295.53
> view matrix models
> #1,0.98551,-0.16953,0.0050399,6.0428,-0.169,-0.97906,0.11345,279.4,-0.014299,-0.11266,-0.99353,283.07
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.98551,-0.16953,0.0050399,5.9321,-0.169,-0.97906,0.11345,277.71,-0.014299,-0.11266,-0.99353,287.18
> fitmap #1 inMap #2
Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc
(#2) using 19295 atoms
average map value = 0.07046, steps = 100
shifted from previous position = 5.39
rotated from previous position = 7.18 degrees
atoms outside contour = 11385, contour level = 0.069238
Position of 9gz1.cif (#1) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99158233 -0.12125120 -0.04541645 3.24555244
-0.12097831 -0.99261687 0.00872005 288.02278951
-0.04613845 -0.00315224 -0.99893009 281.38024575
Axis -0.99789333 0.06068614 0.02293668
Axis point 0.00000000 144.52872247 140.30004746
Rotation angle (degrees) 179.65916390
Shift along axis 20.69420526
> select subtract #1
Nothing selected
> select add #1
19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected
> show sel cartoons
> hide sel atoms
> select subtract #1
Nothing selected
> transparency 50
> volume #2 level 0.0488
> surface dust #2 size 8.3
> volume #2 color #402fbf80
> set bgColor white
> molmap #1 3.0
Opened 9gz1.cif map 3 as #3, grid size 101,163,179, pixel 1, shown at level
0.114, step 1, values float32
> hide #!1 models
> select add #3
2 models selected
> fitmap #3 inMap #2
Fit map 9gz1.cif map 3 in map cryosparc_P30_J395_004_volume_map_sharp.mrc
using 205156 points
correlation = 0.5697, correlation about mean = 0.09812, overlap = 8071
steps = 44, shift = 0.0516, angle = 0.0562 degrees
Position of 9gz1.cif map 3 (#3) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99149066 -0.12176240 -0.04604579 3.40454784
-0.12146155 -0.99255271 0.00928665 287.96926309
-0.04683364 -0.00361484 -0.99889617 281.51410436
Axis -0.99787036 0.06093675 0.02326914
Axis point 0.00000000 144.54374258 140.33239670
Rotation angle (degrees) 179.62960799
Shift along axis 20.70120293
> select subtract #3
Nothing selected
> show #!1 models
> transparency 0
> transparency 50
> color #1 #cc77f6ff
> hide #!2 models
> ui mousemode right translate
> ui tool show "Side View"
> color #3 #f0c1ff80 models
> color #3 #e7d7ff80 models
> color #3 #b427fd80 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> show #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!3 models
> select add #1
19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected
> fitmap #1 inMap #2
Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc
(#2) using 19295 atoms
average map value = 0.07045, steps = 44
shifted from previous position = 0.015
rotated from previous position = 0.00755 degrees
atoms outside contour = 8166, contour level = 0.048797
Position of 9gz1.cif (#1) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99158183 -0.12125347 -0.04542118 3.24815351
-0.12098664 -0.99261700 0.00858869 288.03518042
-0.04612724 -0.00302104 -0.99893101 281.37146891
Axis -0.99789321 0.06068879 0.02293504
Axis point 0.00000000 144.52573033 140.30511965
Rotation angle (degrees) 179.66670158
Shift along axis 20.69246105
> volume #2 level 0.06602
> fitmap #1 inMap #2
Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc
(#2) using 19295 atoms
average map value = 0.07045, steps = 48
shifted from previous position = 0.0217
rotated from previous position = 0.0194 degrees
atoms outside contour = 10972, contour level = 0.066016
Position of 9gz1.cif (#1) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99157472 -0.12127842 -0.04550984 3.26449705
-0.12099626 -0.99261295 0.00891444 287.99740656
-0.04625479 -0.00333282 -0.99892413 281.41657675
Axis -0.99789142 0.06069759 0.02298930
Axis point 0.00000000 144.52990454 140.30505582
Rotation angle (degrees) 179.64839804
Shift along axis 20.69270623
> volume #2 level 0.03923
> fitmap #1 inMap #2
Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc
(#2) using 19295 atoms
average map value = 0.07045, steps = 48
shifted from previous position = 0.00628
rotated from previous position = 0.0107 degrees
atoms outside contour = 6625, contour level = 0.03923
Position of 9gz1.cif (#1) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99159658 -0.12111529 -0.04546788 3.23505125
-0.12083698 -0.99263310 0.00883072 287.99238790
-0.04620246 -0.00326231 -0.99892678 281.40206425
Axis -0.99789690 0.06061648 0.02296554
Axis point 0.00000000 144.52090217 140.30298325
Rotation angle (degrees) 179.65282797
Shift along axis 20.69138696
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.97365,0.0095,-0.22786,13.225,0.0021253,-0.99947,-0.032589,277.27,-0.22805,0.031246,-0.97315,298.85
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.97365,0.0095,-0.22786,16.181,0.0021253,-0.99947,-0.032589,270.07,-0.22805,0.031246,-0.97315,296.87
> fitmap #1 inMap #2
Fit molecule 9gz1.cif (#1) to map cryosparc_P30_J395_004_volume_map_sharp.mrc
(#2) using 19295 atoms
average map value = 0.07046, steps = 160
shifted from previous position = 7.72
rotated from previous position = 13 degrees
atoms outside contour = 6631, contour level = 0.03923
Position of 9gz1.cif (#1) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99156366 -0.12139731 -0.04543366 3.26340974
-0.12111950 -0.99259869 0.00882860 288.01653169
-0.04616916 -0.00325122 -0.99892836 281.39811629
Axis -0.99788865 0.06075841 0.02294881
Axis point 0.00000000 144.53360363 140.30174561
Rotation angle (degrees) 179.65320439
Shift along axis 20.70066034
> ui mousemode right translate
> select subtract #1
Nothing selected
> hide #!1 models
> volume #2 level 0.0775
> show #!1 models
> volume #2 level 0.0488
> volume #2 level 0.08706
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/RealSpaceRefine_84/25HepE525_M_real_space_refined_084.pdb
Chain information for 25HepE525_M_real_space_refined_084.pdb #4
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
> select add #4
18857 atoms, 19214 bonds, 9 pseudobonds, 2338 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> hide #!1 models
> fitmap #4 inMap #2
Fit molecule 25HepE525_M_real_space_refined_084.pdb (#4) to map
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) using 18857 atoms
average map value = 0.09264, steps = 64
shifted from previous position = 1.12
rotated from previous position = 2.3 degrees
atoms outside contour = 11249, contour level = 0.087062
Position of 25HepE525_M_real_space_refined_084.pdb (#4) relative to
cryosparc_P30_J395_004_volume_map_sharp.mrc (#2) coordinates:
Matrix rotation and translation
0.99969266 0.00720946 -0.02371925 1.51432228
-0.00795331 0.99947471 -0.03141731 4.89782055
0.02348029 0.03159630 0.99922487 -5.74779050
Axis 0.78592698 -0.58868858 -0.18911516
Axis point 0.00000000 189.00969684 141.37752898
Rotation angle (degrees) 2.29753035
Shift along axis -0.60614996
> show #!1 models
> select subtract #4
Nothing selected
> hide #!2 models
> dssp
> save
> /Users/ruchigautamsharma/Desktop/25HepE525K/RealSpaceRefine_84/25HepE525Kand9gz1.cxs
> show #!2 models
> show #!3 models
> hide #!2 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> select add #4
18857 atoms, 19214 bonds, 9 pseudobonds, 2338 residues, 2 models selected
> fitmap #4 inMap #3
Fit molecule 25HepE525_M_real_space_refined_084.pdb (#4) to map 9gz1.cif map 3
(#3) using 18857 atoms
average map value = 0.4154, steps = 76
shifted from previous position = 1.04
rotated from previous position = 2.67 degrees
atoms outside contour = 6314, contour level = 0.1138
Position of 25HepE525_M_real_space_refined_084.pdb (#4) relative to 9gz1.cif
map 3 (#3) coordinates:
Matrix rotation and translation
0.99606454 -0.07196877 -0.05172920 37.16173616
-0.07082037 -0.99720741 0.02370289 277.92100606
-0.05329061 -0.01994612 -0.99837981 281.98258680
Axis -0.99901554 0.03573683 0.02628380
Axis point 0.00000000 141.16977199 139.95674169
Rotation angle (degrees) 178.74821600
Shift along axis -19.78156122
> select subtract #4
Nothing selected
> molmap #4 3.0
Opened 25HepE525_M_real_space_refined_084.pdb map 3 as #5, grid size
101,172,182, pixel 1, shown at level 0.117, step 1, values float32
> hide #!4 models
> select add #5
2 models selected
> fitmap #5 inMap #3
Fit map 25HepE525_M_real_space_refined_084.pdb map 3 in map 9gz1.cif map 3
using 198965 points
correlation = 0.6139, correlation about mean = 0.1296, overlap = 4.535e+04
steps = 64, shift = 0.149, angle = 0.23 degrees
Position of 25HepE525_M_real_space_refined_084.pdb map 3 (#5) relative to
9gz1.cif map 3 (#3) coordinates:
Matrix rotation and translation
0.99576399 -0.07550650 -0.05246730 37.82510827
-0.07443085 -0.99697982 0.02216441 278.48945656
-0.05398240 -0.01816533 -0.99837663 281.75419629
Axis -0.99894033 0.03752804 0.02664320
Axis point 0.00000000 141.38144577 139.97071458
Rotation angle (degrees) 178.84333368
Shift along axis -19.82703012
> select subtract #5
Nothing selected
> show #!2 models
> hide #!3 models
> volume #2 level 0.06793
> show #!3 models
> open
> /Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525K/cryosparc_P32_J238_map_sharp.ccp4
Opened cryosparc_P32_J238_map_sharp.ccp4 as #6, grid size 340,340,340, pixel
0.824, shown at level 0.00398, step 2, values float32
> select add #6
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,1.3737,0,1,0,2.1838,0,0,1,14.346
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> view matrix models #6,1,0,0,5.8519,0,1,0,1.9654,0,0,1,47.451
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.84923,-0.51065,0.13432,343.57,0.44513,-0.8292,-0.33805,291.05,0.28401,-0.22729,0.93149,53.587
> view matrix models
> #6,-0.97151,-0.095409,0.21692,280.27,0.013174,-0.9357,-0.35254,373.79,0.23661,-0.33964,0.91031,82.268
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.97151,-0.095409,0.21692,292.09,0.013174,-0.9357,-0.35254,319.62,0.23661,-0.33964,0.91031,69.854
> view matrix models
> #6,-0.97151,-0.095409,0.21692,289.22,0.013174,-0.9357,-0.35254,319.25,0.23661,-0.33964,0.91031,32.472
> ui mousemode right translate
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.97151,-0.095409,0.21692,263.17,0.013174,-0.9357,-0.35254,304.38,0.23661,-0.33964,0.91031,-6.7661
> view matrix models
> #6,-0.97151,-0.095409,0.21692,264.54,0.013174,-0.9357,-0.35254,302.04,0.23661,-0.33964,0.91031,-0.13825
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.97856,-0.10049,0.17976,271.31,0.040104,-0.94915,-0.31227,295.11,0.202,-0.29837,0.93283,-5.0426
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.97856,-0.10049,0.17976,248.82,0.040104,-0.94915,-0.31227,288.51,0.202,-0.29837,0.93283,-12.033
> ui mousemode right "rotate selected models"
> view matrix models
> #6,-0.99321,-0.077804,-0.086483,282.06,0.1096,-0.87511,-0.47136,286.76,-0.039008,-0.47764,0.87769,60.584
> ui mousemode right "translate selected models"
> view matrix models
> #6,-0.99321,-0.077804,-0.086483,282.11,0.1096,-0.87511,-0.47136,293.55,-0.039008,-0.47764,0.87769,66.939
> select add #6
3 models selected
> hide #!5 models
> hide #!2 models
> fitmap #6 inMap #3
Fit map cryosparc_P32_J238_map_sharp.ccp4 in map 9gz1.cif map 3 using 48792
points
correlation = 0.5714, correlation about mean = 0.2739, overlap = 3767
steps = 176, shift = 6.29, angle = 12 degrees
Position of cryosparc_P32_J238_map_sharp.ccp4 (#6) relative to 9gz1.cif map 3
(#3) coordinates:
Matrix rotation and translation
-0.98705424 -0.15347550 -0.04657448 313.25053616
-0.15837539 0.88683136 0.43410522 -14.96375182
-0.02532080 0.43586165 -0.89965741 224.60374361
Axis 0.08026911 -0.97129511 -0.22392562
Axis point 155.38113418 0.00000000 114.91132655
Rotation angle (degrees) 179.37312029
Shift along axis -10.61597105
> hide #!3 models
> show #!3 models
> select add #6
4 models selected
> select subtract #6
Nothing selected
> show #!1 models
> hide #!3 models
> transparency #6.1 50
> select add #6
4 models selected
> fitmap #1 inMap #6
Fit molecule 9gz1.cif (#1) to map cryosparc_P32_J238_map_sharp.ccp4 (#6) using
19295 atoms
average map value = 0.1538, steps = 44
shifted from previous position = 0.175
rotated from previous position = 0.425 degrees
atoms outside contour = 4244, contour level = 0.0039782
Position of 9gz1.cif (#1) relative to cryosparc_P32_J238_map_sharp.ccp4 (#6)
coordinates:
Matrix rotation and translation
-0.98581921 -0.16532541 -0.02877541 313.70000276
-0.16128802 0.88612176 0.43448179 -35.11481203
-0.04633236 0.43296162 -0.90022085 223.35351858
Axis -0.08408408 0.97111249 0.22331680
Axis point 155.85507876 0.00000000 114.98629567
Rotation angle (degrees) 179.48206162
Shift along axis -10.59901475
> select subtract #6
Nothing selected
> volume #6 level 0.0163
> show #!3 models
> hide #!3 models
> volume #6 level 0.1231
> show #!2 models
> hide #!2 models
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right translate
> select ::name="XB2"
40 atoms, 42 bonds, 2 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 40 atom styles
> show #!2 models
> volume #2 level 0.09663
> show #!3 models
> hide #!2 models
> volume #3 level 0.8202
> select add #1
19295 atoms, 19651 bonds, 17 pseudobonds, 2393 residues, 3 models selected
> select subtract #1
Nothing selected
> save "/Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525K/mava9gZ1 and
> 25HepE525K.cxs"
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!2 models
> hide #!6 models
> show #!3 models
> hide #!3 models
> show #!6 models
> hide #!2 models
> show #!2 models
> save "/Users/ruchigautamsharma/Desktop/25HepE525K/25HepE525K/mava9gZ1 and
> 25HepE525Kand.cxs"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> hide #!6 models
> volume #2 level 0.05836
> show #!6 models
> hide #!2 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-22.5.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i7
Processor Speed: 1.7 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 580.140.1~51
Software:
System Software Overview:
System Version: macOS 14.7.1 (23H222)
Kernel Version: Darwin 23.6.0
Time since boot: 2 days, 2 hours, 19 minutes
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
DELL P2419H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: H1F7ZR2
Mirror: Off
Online: Yes
Rotation: Supported
Adapter Type: DVI or HDMI
Adapter Firmware Version: 15.67
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 2.4.1
Babel: 2.15.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 2.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.17
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.7
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.57.1
ChimeraX-AtomicLibrary: 14.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.4.6
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.12.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.7
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.23.1
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.4
ChimeraX-DiffPlot: 1.0
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMalign: 0.1.1
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-LigandRecognizer: 0.2
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.3.7
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-QScore: 1.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
finufft: 2.3.1
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
Send2Trash: 1.8.3
SEQCROW: 1.8.17
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 6 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash moving window between screens |
comment:2 by , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
This ChimeraX crash is caused by a bug in the Qt window toolkit used by ChimeraX and happens on Mac with multiple displays. The crash sometimes happens when plugging in or unplugging an external display, waking from sleep, or moving windows between screens. The ChimeraX daily build uses a newer version of Qt and we have not seen these multi-display Mac crashes in the newer version so you may want to try it.