![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16787 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-arm64-arm-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
Thread 0x00000003f5df7000 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001e85e4f40 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, 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.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, psutil._psutil_osx, psutil._psutil_posix, chimerax.atom_search.ast, chimerax.chem_group._chem_group, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 129)
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{
"uptime" : 100000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "Mac15,6",
"coalitionID" : 786,
"osVersion" : {
"train" : "macOS 14.7",
"build" : "23H124",
"releaseType" : "User"
},
"captureTime" : "2025-02-05 14:04:46.6663 +0100",
"codeSigningMonitor" : 1,
"incident" : "6AAF7B2D-C3A7-49FB-A4A6-74B1E38D18D2",
"pid" : 20042,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-05 09:07:42.7206 +0100",
"procStartAbsTime" : 1999690737239,
"procExitAbsTime" : 2427467412741,
"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":"CF9CF97E-A2E3-504A-90A5-D49E51797F4B","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C52F2DF2-D8F2-7ECA-B0AF-1AE4DA9AFA72",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"wakeTime" : 18620,
"sleepWakeUUID" : "958983AE-BE83-413D-B9F7-3209326D3F52",
"sip" : "enabled",
"vmRegionInfo" : "0x4627108f1ad8 is not in any region. Bytes after previous region: 76652559145689 Bytes before following region: 28419520783656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x00004627108f1ad8","rawCodes":[1,77133595482840],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00004627108f1ad8"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":20042},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x4627108f1ad8 is not in any region. Bytes after previous region: 76652559145689 Bytes before following region: 28419520783656\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
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"faultingThread" : 0,
"threads" : 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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/_datetime.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/lib-dynload\/math.cpython-311-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/Python",
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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/laschnei/Documents/KBTBD4/Models/250205_Sym_befIso.pdb
Chain information for 250205_Sym_befIso.pdb #1
---
Chain | Description
A B | No description available
C D | No description available
> open
> /Users/laschnei/Documents/KBTBD4/Models/cryosparc_P2_J429_004_volume_map_sharp.mrc
Opened cryosparc_P2_J429_004_volume_map_sharp.mrc as #2, grid size
256,256,256, pixel 1.08, shown at level 0.0684, step 1, values float32
> set bgColor white
> volume #2 level 0.1094
> surface dust #2 size 10.8
> select #1
17100 atoms, 17410 bonds, 2180 residues, 1 model selected
> show sel atoms
> ui tool show "Add Hydrogens"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> addh #1
Summary of feedback from adding hydrogens to 250205_Sym_befIso.pdb #1
---
notes | Termini for 250205_Sym_befIso.pdb (#1) chain A determined from SEQRES records
Termini for 250205_Sym_befIso.pdb (#1) chain B determined from SEQRES records
Termini for 250205_Sym_befIso.pdb (#1) chain C determined from SEQRES records
Termini for 250205_Sym_befIso.pdb (#1) chain D determined from SEQRES records
Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini: /A SER 26, /B SER 26, /C
SER 21, /D SER 21
Chain-final residues that are actual C termini: /A ALA 534, /B ALA 534, /C ALA
601, /D ALA 601
Chain-final residues that are not actual C termini:
2269 hydrogen bonds
Adding 'H' to /A SER 26
Adding 'H' to /B SER 26
Adding 'H' to /C SER 21
Adding 'H' to /D SER 21
17182 hydrogens added
> volume #2 color #b2b2b279
> ~select
Nothing selected
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
Chain information for 250205_Sym_befIso.pdb
---
Chain | Description
1.2/A 1.2/B | No description available
1.2/C 1.2/D | No description available
> clipper associate #2 toModel #1
Opened cryosparc_P2_J429_004_volume_map_sharp.mrc as #1.1.1.1, grid size
256,256,256, pixel 1.08, shown at step 1, values float32
> isolde sim start /A,C,B,D
ISOLDE: started sim
> ui tool show "Ramachandran Plot"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 44 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> hide #1.3 models
> show #1.3 models
> hide #!1.2 models
> show #!1.2 models
> hide #!1.1 models
> save /Users/laschnei/Documents/KBTBD4/Models/250205_Sym_afIso.pdb
> open /Users/laschnei/Documents/KBTBD4/Models/250205_Sym_afIso.pdb
Chain information for 250205_Sym_afIso.pdb #2
---
Chain | Description
A B | No description available
C D | No description available
> open
> /Users/laschnei/Documents/KBTBD4/Models/cryosparc_P2_J429_004_volume_map_sharp.mrc
Opened cryosparc_P2_J429_004_volume_map_sharp.mrc as #3, grid size
256,256,256, pixel 1.08, shown at level 0.0684, step 1, values float32
> surface dust #3 size 10.8
> volume #3 level 0.08598
> hide #!1 models
> hide #!1.2 models
> hide #1.3 models
> volume #3 color #ffffb284
> volume #3 color #ffffb285
> volume #3 level 0.1094
> open /Users/laschnei/Documents/KBTBD4/Models/250128_K4dim_PP2AAdim.pdb
Chain information for 250128_K4dim_PP2AAdim.pdb #4
---
Chain | Description
A B | No description available
C D E F | No description available
> hide #2,4 atoms
> show #2,4 cartoons
> hide #2 models
> close #1.3#1#1.1-2
> hide #4 models
> hide #!3 models
> show #2 models
> show #4 models
> close #4
> color #2/A light cyan
> color #2/A light blue
> color #2/B steel blue
> color #2/C hot pink
> color #2/D light pink
> show #!3 models
> color zone #3 near #2 distance 5
> transparency #3 50
> save
> /Users/laschnei/Documents/KBTBD4/Models/250205_K4dim_PAdim_improvedModel.cxs
> includeMaps true
> ui tool show "Side View"
> volume #3 level 0.1153
> color zone #3 near #2 distance 5
> view #1
No objects specified.
> view #2
> transparency #3 50
> show sel atoms
> show #!3 models
> open /Users/laschnei/Downloads/cryosparc_P2_J491_003_volume_map_sharp.mrc
Opened cryosparc_P2_J491_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.0715, step 1, values float32
> open /Users/laschnei/Downloads/cryosparc_P2_J491_003_volume_map_sharp.mrc
Opened cryosparc_P2_J491_003_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.08, shown at level 0.0715, step 1, values float32
> surface dust #3 size 10.8
> surface dust #1 size 10.8
> surface dust #4 size 10.8
> close #4
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui tool show "Fit in Map"
> fitmap #1 inMap #3
Fit map cryosparc_P2_J491_003_volume_map_sharp.mrc in map
cryosparc_P2_J429_004_volume_map_sharp.mrc using 167634 points
correlation = 0.3133, correlation about mean = 0.08974, overlap = 807.7
steps = 160, shift = 9.66, angle = 6 degrees
Position of cryosparc_P2_J491_003_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99979955 -0.01906381 0.00611867 9.48960351
0.01959116 0.99453158 -0.10258227 17.60071371
-0.00412961 0.10268158 0.99470570 -13.45091711
Axis 0.98154544 0.04900597 0.18484309
Axis point 0.00000000 153.07725452 159.74234359
Rotation angle (degrees) 6.00190696
Shift along axis 7.69070800
> fitmap #1 inMap #3
Fit map cryosparc_P2_J491_003_volume_map_sharp.mrc in map
cryosparc_P2_J429_004_volume_map_sharp.mrc using 167634 points
correlation = 0.3133, correlation about mean = 0.08972, overlap = 807.7
steps = 44, shift = 0.00324, angle = 0.00981 degrees
Position of cryosparc_P2_J491_003_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
0.99980183 -0.01893677 0.00614054 9.46948138
0.01946657 0.99454551 -0.10247088 17.59799976
-0.00416658 0.10257011 0.99471705 -13.43197689
Axis 0.98171091 0.04934924 0.18387045
Axis point 0.00000000 152.98352373 159.88747298
Rotation angle (degrees) 5.99435241
Shift along axis 7.69499740
> select #1
2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.9998,-0.018937,0.0061405,-10.6,0.019467,0.99455,-0.10247,42.093,-0.0041666,0.10257,0.99472,19.498
> view matrix models
> #1,0.9998,-0.018937,0.0061405,-5.8056,0.019467,0.99455,-0.10247,18.443,-0.0041666,0.10257,0.99472,23.755
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.8647,0.14721,-0.48023,47.799,-0.31578,0.90284,-0.29184,100.01,0.39061,0.404,0.82717,-52.544
> view matrix models
> #1,0.39958,0.44617,0.80079,-81.721,-0.91355,0.12147,0.38817,209.71,0.075919,-0.88667,0.45614,213.55
> view matrix models
> #1,-0.66768,-0.70428,0.24124,291.46,-0.33188,-0.0084839,-0.94329,305.76,0.66638,-0.70987,-0.22807,188.93
> fitmap #1 inMap #3
Fit map cryosparc_P2_J491_003_volume_map_sharp.mrc in map
cryosparc_P2_J429_004_volume_map_sharp.mrc using 167634 points
correlation = 0.9136, correlation about mean = 0.6863, overlap = 4949
steps = 144, shift = 16.9, angle = 7.3 degrees
Position of cryosparc_P2_J491_003_volume_map_sharp.mrc (#1) relative to
cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.68390166 -0.71669623 0.13647352 306.45011025
-0.30796929 0.11401773 -0.94453950 295.47043720
0.66138750 -0.68800179 -0.29869735 209.46705236
Axis 0.35978805 -0.73617940 0.57322984
Axis point 200.12462599 0.00000000 257.55312466
Rotation angle (degrees) 159.11384359
Shift along axis 12.81060353
> ui mousemode right zoom
> volume #1 level 0.0936
> ~select
Nothing selected
> volume #1 level 0.1618
> show #!3 models
> hide #2 models
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select clear
> show #2 models
> hide #!1 models
> show sel atoms
> ui tool show "Add Hydrogens"
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> select H
17182 atoms, 2180 residues, 1 model selected
> hide sel atoms
> ~select
Nothing selected
> show sel atoms
> ~select
Nothing selected
> hide sel atoms
> ~hbonds
> select H
17182 atoms, 2180 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #!3 models
> hide #!3 models
> show #!1 models
> view #1
> hide #!1 models
> show sel atoms
> ~select
Nothing selected
> volume #1 color #b2ffff80
> ~select
Nothing selected
> open /Users/laschnei/Downloads/cryosparc_P2_J493_003_volume_map_sharp.mrc
Opened cryosparc_P2_J493_003_volume_map_sharp.mrc as #4, grid size
256,256,256, pixel 1.08, shown at level 0.0723, step 1, values float32
> select #4
4 models selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.38204,-0.83949,-0.3864,253.44,0.073121,0.44426,-0.89291,186.78,0.92125,0.31287,0.23111,-67.216
> view matrix models
> #4,-0.60725,-0.40434,-0.68393,370.05,0.68182,0.17672,-0.70986,115.01,0.40789,-0.89737,0.16837,179.49
> view matrix models
> #4,-0.67912,-0.23034,-0.69695,357.68,0.42658,0.64883,-0.63012,74.303,0.59734,-0.72523,-0.34237,198.18
> view matrix models
> #4,-0.52274,-0.84683,-0.098098,340.76,-0.32249,0.30295,-0.89678,261.53,0.78914,-0.43715,-0.43146,143.82
> view matrix models
> #4,-0.47982,-0.87102,-0.10537,339.15,-0.21069,0.23098,-0.94987,263.16,0.85169,-0.43357,-0.29434,116.24
> fitmap #4 inMap #3
Fit map cryosparc_P2_J493_003_volume_map_sharp.mrc in map
cryosparc_P2_J429_004_volume_map_sharp.mrc using 167662 points
correlation = 0.9135, correlation about mean = 0.6818, overlap = 4972
steps = 248, shift = 32.3, angle = 20.4 degrees
Position of cryosparc_P2_J493_003_volume_map_sharp.mrc (#4) relative to
cryosparc_P2_J429_004_volume_map_sharp.mrc (#3) coordinates:
Matrix rotation and translation
-0.68562517 -0.71504712 0.13647620 306.44510486
-0.30763011 0.11468864 -0.94456881 295.45044861
0.65975893 -0.68960434 -0.29860344 209.94018074
Axis 0.35884860 -0.73649193 0.57341724
Axis point 199.94170787 0.00000000 257.61539199
Rotation angle (degrees) 159.19101567
Shift along axis 12.75384501
> ui mousemode right translate
> ui mousemode right rotate
> surface dust #4 size 10.8
> volume #4 level 0.1556
> hide #2 models
> color zone #4 near #2 distance 4
> color zone #4 near #2 distance 3
> color zone #4 near #2 distance 3.5
> color zone #4 near #2 distance 4
> color zone #4 near #2 distance 4.5
> color zone #4 near #2 distance 6
> color zone #4 near #2 distance 4
> color zone #4 near #2 distance 3
> color zone #4 near #2 distance 4
> show #2 models
> hide #!4 models
> show sel atoms
> show #!4 models
> hide #!4 models
> select clear
> show sel atoms
> select #2/C #2/D
9052 atoms, 9188 bonds, 1162 residues, 1 model selected
> show sel atoms
> color sel byhetero
> ~sel]
Unknown command: ~sel]
> ~select
Nothing selected
> ui tool show Distances
> distance /C:544@NE2 /D:76@OE2
Distance between /C GLN 544 NE2 and /D GLU 76 OE2: 4.638Å
> distance /D:238@OE2 /C:588@NZ
Distance between /D GLU 238 OE2 and /C LYS 588 NZ: 5.441Å
> distance /D:277@OD2 /C:592@NE2
Distance between /D ASP 277 OD2 and /C GLN 592 NE2: 7.171Å
> distance /D:273@OH /C:585@SD
Distance between /D TYR 273 OH and /C MET 585 SD: 4.958Å
> distance /C:589@OH /D:316@NE2
Distance between /C TYR 589 OH and /D HIS 316 NE2: 4.943Å
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> distance /D:589@OH /C:316@NE2
Distance between /D TYR 589 OH and /C HIS 316 NE2: 5.963Å
> show #!4 models
> hide #!5 models
> hide #5.1 models
> show #5.1 models
> hide #!4 models
> select clear
> distance /C:76@OE2 /D:544@NE2
Distance between /C GLU 76 OE2 and /D GLN 544 NE2: 2.848Å
> show #!4 models
> hide #!4 models
> show #!4 models
> volume #4 color #937193
> volume #4 color #93719352
> distance /C:122@OE2 /D:578@NZ
Distance between /C GLU 122 OE2 and /D LYS 578 NZ: 5.553Å
> volume #4 level 0.1253
> hide #!4 models
> distance /C:270@NH1 /D:585@SD
Distance between /C ARG 270 NH1 and /D MET 585 SD: 5.185Å
> show #!4 models
> hide #!5 models
> hide #5.1 models
> hide #2 models
> show #2 models
> volume #4 color #d09fd0a1
> hide #!4 models
> show #!5 models
> show #5.1 models
> ui tool show "Side View"
===== 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
> open /Users/laschnei/Downloads/cryosparc_P2_J497_003_volume_map_sharp.mrc
Opened cryosparc_P2_J497_003_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.08, shown at level 0.0794, step 1, values float32
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
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: Mac15,6
Model Number: Z1AV000M7SM/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.1.1
OS Loader Version: 10151.140.19.700.2
Software:
System Software Overview:
System Version: macOS 14.7 (23H124)
Kernel Version: Darwin 23.6.0
Time since boot: 3 days, 2 hours, 37 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
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
DELL P2725H:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 100.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.8
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.10
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.3
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.1
ChimeraX-MedicalToolbar: 1.0.3
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.17
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.5
ChimeraX-PDB: 2.7.5
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.4.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.0.15
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.2
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.16.5
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.39.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.3
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.2.1
cxservices: 1.2.2
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.1
decorator: 5.1.1
docutils: 0.20.1
executing: 2.0.1
filelock: 3.13.4
fonttools: 4.53.0
funcparserlib: 2.0.0a0
glfw: 2.7.0
grako: 3.16.5
h5py: 3.11.0
html2text: 2024.2.26
idna: 3.7
ihm: 1.0
imagecodecs: 2024.1.1
imagesize: 1.4.1
ipykernel: 6.29.2
ipython: 8.21.0
ipywidgets: 8.1.3
jedi: 0.19.1
jinja2: 3.1.4
jupyter-client: 8.6.0
jupyter-core: 5.7.2
jupyterlab-widgets: 3.0.11
kiwisolver: 1.4.5
line-profiler: 4.1.2
lxml: 5.2.1
lz4: 4.3.3
MarkupSafe: 2.1.5
matplotlib: 3.8.4
matplotlib-inline: 0.1.7
msgpack: 1.0.8
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.0
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.3.0
pip: 24.0
pkginfo: 1.10.0
platformdirs: 4.2.2
prompt-toolkit: 3.0.47
psutil: 5.9.8
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pygments: 2.17.2
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.1.2
pyproject-hooks: 1.1.0
PyQt6-commercial: 6.6.1
PyQt6-Qt6: 6.6.3
PyQt6-sip: 13.6.0
PyQt6-WebEngine-commercial: 6.6.0
PyQt6-WebEngine-Qt6: 6.6.3
python-dateutil: 2.9.0.post0
pytz: 2024.1
pyzmq: 26.0.3
qtconsole: 5.5.1
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.13.0
setuptools: 69.5.1
setuptools-scm: 8.0.4
sfftk-rw: 0.8.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 7.2.6
sphinx-autodoc-typehints: 2.0.1
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2024.1.30
tinyarray: 1.2.4
tornado: 6.4.1
traitlets: 5.14.2
typing-extensions: 4.12.2
tzdata: 2024.1
urllib3: 2.2.1
wcwidth: 0.2.13
webcolors: 1.13
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.11
Change History (2)
comment:1 by , 9 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 , 9 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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