![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 3 months ago
Closed 3 months ago
#18160 closed defect (duplicate)
Graphics hardware encountered an error and was reset
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.5-x86_64-i386-64bit
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff84792afc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 1689 in set_multishadow_view
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 251 in _draw_scene
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 188 in draw
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 84 in draw_new_frame
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
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.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, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, scipy._lib._ccallback_c, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.optimize._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.special._ufuncs_cxx, scipy.special._cdflib, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix (total: 122)
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{
"uptime" : 24000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,4",
"coalitionID" : 477,
"osVersion" : {
"train" : "macOS 14.5",
"build" : "23F79",
"releaseType" : "User"
},
"captureTime" : "2025-07-09 18:45:41.9739 -0500",
"codeSigningMonitor" : 0,
"incident" : "6ED4BFB8-6C0B-42D7-BCAB-256C50ACFF23",
"pid" : 453,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-07-08 23:55:53.6221 -0500",
"procStartAbsTime" : 16880698549,
"procExitAbsTime" : 24290726362792,
"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":"56925B66-3E6E-5128-9967-9516FB06FFC8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "85818EB2-F3CC-7766-5728-F17B5EE8A795",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 328,
"bridgeVersion" : {"build":"21P5077","train":"8.5"},
"sleepWakeUUID" : "8E5C8873-A699-45F8-8421-6B08EAF90410",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":453},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"base" : 140703195389952,
"size" : 25769803776,
"uuid" : "b48cfc6b-b7ed-3343-97fb-f5187dc04df8"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=3.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG image 396K 33 \nColorSync 252K 31 \nCoreAnimation 1104K 117 \nCoreGraphics 12K 2 \nCoreServices 196K 1 \nCoreUI image data 5132K 38 \nFoundation 32K 2 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 2.7G 743 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_REALLOC (reserved) 4K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 152K 38 \nStack 169.8M 39 \nStack Guard 56.0M 1 \nVM_ALLOCATE 352.1M 204 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 48.3M 897 \n__DATA_CONST 53.3M 463 \n__DATA_DIRTY 1842K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 226.8M 246 \n__OBJC_RO 71.8M 1 \n__OBJC_RW 2200K 2 \n__TEXT 1.1G 891 \ndyld private memory 648K 8 \nmapped file 532.0M 94 \nshared memory 2996K 28 \n=========== ======= ======= \nTOTAL 5.4G 4137 \nTOTAL, minus reserved VM space 5.3G 4137 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "89fa80d30342b1b4a18d27affafa1b0f44fdef7c",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "60186475825c62000ccf5450",
"factorPackIds" : {
},
"deploymentId" : 240000083
},
{
"rolloutId" : "64628732bf2f5257dedc8988",
"factorPackIds" : {
},
"deploymentId" : 240000001
}
],
"experiments" : [
{
"treatmentId" : "28060e10-d4e5-4163-aa2b-d8bd088d5cbf",
"experimentId" : "6685b283afc7c17197d69eec",
"deploymentId" : 400000011
}
]
}
}
===== 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/naseeriqbal/Desktop/HFLK.cxs format session
opened ChimeraX session
> open 9CZ2 fromDatabase pdb format mmcif
Summary of feedback from opening 9CZ2 fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /XB:1
Atom H1 is not in the residue template for MET /XD:1
Atom H1 is not in the residue template for MET /XF:1
Atom H1 is not in the residue template for MET /XH:1
Atom H1 is not in the residue template for MET /XJ:1
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
9cz2 title:
Cryo-EM structure of a nautilus-like HflK/C assembly in complex with FtsH AAA
protease [more info...]
Chain information for 9cz2 #2
---
Chain | Description | UniProt
A B C D E F G H I J K L | ATP-dependent zinc metalloprotease FtsH | C3SSK2_ECOLX 1-644
XA XC XE XG XI XK XM XO XQ XS XU XW | Modulator of FtsH protease HflK | C3SG32_ECOLX 1-419
XB XD XF XH XJ XL XN XP XR XT XV XX | Modulator of FtsH protease HflC | A0A376L393_ECOLX 1-334
> select add #1
3202 atoms, 3252 bonds, 419 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> ui tool show "Side View"
> hide #!2 models
> show #!2 models
> show #1 target m
> hide #1 models
> select add #2
114310 atoms, 115166 bonds, 10 pseudobonds, 7130 residues, 2 models selected
> show #!2 target m
> close session
> open 9CZ2 fromDatabase pdb format mmcif
Summary of feedback from opening 9CZ2 fetched from pdb
---
warnings | Atom H1 is not in the residue template for MET /XB:1
Atom H1 is not in the residue template for MET /XD:1
Atom H1 is not in the residue template for MET /XF:1
Atom H1 is not in the residue template for MET /XH:1
Atom H1 is not in the residue template for MET /XJ:1
4 messages similar to the above omitted
Too many hydrogens missing from residue template(s) to warn about
9cz2 title:
Cryo-EM structure of a nautilus-like HflK/C assembly in complex with FtsH AAA
protease [more info...]
Chain information for 9cz2 #1
---
Chain | Description | UniProt
A B C D E F G H I J K L | ATP-dependent zinc metalloprotease FtsH | C3SSK2_ECOLX 1-644
XA XC XE XG XI XK XM XO XQ XS XU XW | Modulator of FtsH protease HflK | C3SG32_ECOLX 1-419
XB XD XF XH XJ XL XN XP XR XT XV XX | Modulator of FtsH protease HflC | A0A376L393_ECOLX 1-334
> show atoms
> hide atoms
> show cartoons
> ui tool show "Show Sequence Viewer"
> sequence chain /XA
Alignment identifier is 1/XA
> select /XA:79-96,169-175,179-224,244-337
2612 atoms, 2626 bonds, 165 residues, 1 model selected
> select clear
> select /XA:97-100,107-109,114-117,121-124,131-132,143-150,156-166,232-240
728 atoms, 728 bonds, 45 residues, 1 model selected
> select clear
> select /XA:338-355
291 atoms, 291 bonds, 18 residues, 1 model selected
> ui mousemode right zoom
> select clear
> select /XA:79-114
569 atoms, 574 bonds, 36 residues, 1 model selected
> ui mousemode right zoom
> select /XA:97-100,107-109,114-117,121-124,131-132,143-150,156-166,232-240
728 atoms, 728 bonds, 45 residues, 1 model selected
> select /XA:161
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /XA:161-162
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /XA:161
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /XA:161
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /XA:229
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /XA:229
17 atoms, 16 bonds, 1 residue, 1 model selected
> select /XA:226
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:226-227
35 atoms, 36 bonds, 2 residues, 1 model selected
> select /XA:226
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:226
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:151
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /XA:151-154
52 atoms, 51 bonds, 4 residues, 1 model selected
> select /XA:97-100,107-109,114-117,121-124,131-132,143-150,156-166,232-240
728 atoms, 728 bonds, 45 residues, 1 model selected
> select /XA:150
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /XA:150
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /XA:150-152
44 atoms, 43 bonds, 3 residues, 1 model selected
> select /XA:150-152
44 atoms, 43 bonds, 3 residues, 1 model selected
> select /XA:151
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /XA:151
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /XA:241
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XA:241
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XA:243
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:243
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:139
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XA:139
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XA:134
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:134
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:139
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XA:139
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XA:126
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:126-127
28 atoms, 28 bonds, 2 residues, 1 model selected
> select /XA:127
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /XA:127
14 atoms, 13 bonds, 1 residue, 1 model selected
> select /XA:128
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /XA:128
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /XA:79-96,169-175,179-224,244-337
2612 atoms, 2626 bonds, 165 residues, 1 model selected
> select /XA:298
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /XA:298
19 atoms, 18 bonds, 1 residue, 1 model selected
> select /XA:305
16 atoms, 15 bonds, 1 residue, 1 model selected
> select /XA:305-306
26 atoms, 25 bonds, 2 residues, 1 model selected
> select /XA:79-96,169-175,179-224,244-337
2612 atoms, 2626 bonds, 165 residues, 1 model selected
> select /XA:307
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /XA:307-314
143 atoms, 144 bonds, 8 residues, 1 model selected
> select /XA:324
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:324-328
98 atoms, 98 bonds, 5 residues, 1 model selected
> ui tool show Distances
> select /XB:244
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add /XC:280
29 atoms, 27 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select subtract /XB:244
14 atoms, 13 bonds, 1 residue, 1 model selected
> select add /XB:244
29 atoms, 27 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> ui tool show "Model Panel"
> select clear
Exactly two atoms must be selected!
> ui tool show "Show Sequence Viewer"
> sequence chain /XE
Alignment identifier is 1/XE
> select clear
> select /XA:138-139
25 atoms, 24 bonds, 2 residues, 1 model selected
> select /XA:138-144
109 atoms, 108 bonds, 7 residues, 1 model selected
> select /XA:138
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:138
15 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA
4404 atoms, 4438 bonds, 277 residues, 1 model selected
> select /XE
4404 atoms, 4438 bonds, 277 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,16.964,0,1,0,14.783,0,0,1,28.762
> view matrix models #1,1,0,0,29.875,0,1,0,39.693,0,0,1,55.648
> select add #1
114310 atoms, 115166 bonds, 10 pseudobonds, 7130 residues, 2 models selected
> select subtract #1
Nothing selected
> select /XA:110
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /XA:110-113
73 atoms, 73 bonds, 4 residues, 1 model selected
> view matrix models #1,1,0,0,28.986,0,1,0,36.543,0,0,1,48.019
> view matrix models #1,1,0,0,30.397,0,1,0,30.516,0,0,1,50.869
> view matrix models #1,1,0,0,18.885,0,1,0,44.786,0,0,1,52.841
> view matrix models #1,1,0,0,11.792,0,1,0,53.94,0,0,1,53.776
> view matrix models #1,1,0,0,19.27,0,1,0,69.273,0,0,1,71.117
> view matrix models #1,1,0,0,16.697,0,1,0,57.761,0,0,1,45.982
> ui mousemode right zoom
> select /XA:128
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /XA:128
20 atoms, 20 bonds, 1 residue, 1 model selected
> select /XA:134
14 atoms, 14 bonds, 1 residue, 1 model selected
> select /XA:134-135
30 atoms, 30 bonds, 2 residues, 1 model selected
> select /XR:229
10 atoms, 9 bonds, 1 residue, 1 model selected
> select add /XS:267
25 atoms, 23 bonds, 2 residues, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,33.48,0,1,0,75.757,0,0,1,33.131
> view matrix models #1,1,0,0,43.56,0,1,0,86.564,0,0,1,25.412
> view matrix models #1,1,0,0,53.921,0,1,0,97.024,0,0,1,15.969
> view matrix models #1,1,0,0,50.021,0,1,0,85.849,0,0,1,2.7545
> ui mousemode right zoom
> select clear
> select /XR:237
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add /XQ:257
34 atoms, 32 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select /XR:237
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /XR:233
10 atoms, 9 bonds, 1 residue, 1 model selected
> select /XR:237
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add /XR:233
34 atoms, 32 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> select clear
> select /XR:237
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add /XS:267
39 atoms, 37 bonds, 2 residues, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select subtract /XS:267
24 atoms, 23 bonds, 1 residue, 1 model selected
> select add /XS:267
39 atoms, 37 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
No distances to delete!
> select subtract /XR:237
15 atoms, 14 bonds, 1 residue, 1 model selected
> select add /XR:237
39 atoms, 37 bonds, 2 residues, 1 model selected
Exactly two atoms must be selected!
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,50.886,0,1,0,87.389,0,0,1,65.988
> view matrix models #1,1,0,0,54.76,0,1,0,91.626,0,0,1,90.708
> view matrix models #1,1,0,0,50.237,0,1,0,86.786,0,0,1,72.349
> ui mousemode right zoom
> ui tool show "Show Sequence Viewer"
> sequence chain /XI
Alignment identifier is 1/XI
> select
> /XI:97-100,104-105,107-109,114-117,121-124,135-136,141-150,156-166,232-240
805 atoms, 804 bonds, 49 residues, 1 model selected
> select /XI:141
24 atoms, 23 bonds, 1 residue, 1 model selected
> select /XI:141
24 atoms, 23 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,32.404,0,1,0,90.181,0,0,1,87.391
> view matrix models #1,1,0,0,18.83,0,1,0,92.715,0,0,1,98.641
> view matrix models #1,1,0,0,4.9744,0,1,0,94.493,0,0,1,106.89
> view matrix models #1,1,0,0,-3.8155,0,1,0,95.997,0,0,1,113.63
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,-6.7711,0,1,0,130.22,0,0,1,106.53
> view matrix models #1,1,0,0,-11.926,0,1,0,171.16,0,0,1,91.259
> ui mousemode right zoom
> select /XI:137-138
31 atoms, 30 bonds, 2 residues, 1 model selected
> select /XI:137-140
57 atoms, 56 bonds, 4 residues, 1 model selected
> open "/Users/naseeriqbal/Downloads/cryosparc_P32_J56_class_00_final_volume
> (1).mrc"
Opened cryosparc_P32_J56_class_00_final_volume (1).mrc as #2, grid size
192,192,192, pixel 2.91, shown at level 0.0776, step 1, values float32
> hide #!2 models
> hide #!1 models
> show #!2 models
> open
> /Users/naseeriqbal/Downloads/cryosparc_P32_J56_class_00_final_volume.mrc
Opened cryosparc_P32_J56_class_00_final_volume.mrc as #3, grid size
192,192,192, pixel 2.91, shown at level 0.0776, step 1, values float32
===== 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/naseeriqbal/Downloads/cryosparc_P32_J56_class_00_final_volume.mrc
Opened cryosparc_P32_J56_class_00_final_volume.mrc as #1, grid size
192,192,192, pixel 2.91, shown at level 0.0776, step 1, values float32
OpenGL version: 4.1 INTEL-22.5.11
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 i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0)
OS Loader Version: 580~2215
Software:
System Software Overview:
System Version: macOS 14.5 (23F79)
Kernel Version: Darwin 23.5.0
Time since boot: 9 hours, 41 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: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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 , 3 months ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 3 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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