![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 months ago
Closed 6 months ago
#17436 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-14.6.1-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: Aborted
Current thread 0x00007ff851183dc0 (most recent call first):
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 248 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 556 in swap_buffers
File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 202 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, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.pdb._pdbio, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, chimerax.atom_search.ast (total: 124)
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{
"uptime" : 160000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 493,
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"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2025-04-19 18:10:33.5311 +0100",
"codeSigningMonitor" : 0,
"incident" : "EF341AC5-3633-4F33-99CE-EF349F8F9442",
"pid" : 69762,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-04-19 17:03:57.7095 +0100",
"procStartAbsTime" : 158734410559979,
"procExitAbsTime" : 162730141166865,
"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":"DC5D67F2-7ADE-58F9-9F5E-DB73CCFB0CB7","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "297556F7-04EA-3C51-2CFA-783C8E54CBDB",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 12302,
"bridgeVersion" : {"build":"21P6074","train":"8.6"},
"sleepWakeUUID" : "289D754F-3981-44B2-A237-4F3AED7C27C6",
"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":69762},
"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\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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"CFBundleVersion" : "21.0.19"
},
{
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"arch" : "x86_64",
"base" : 140703417286656,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 21172216,
"uuid" : "d0e19a37-f677-32b5-b3d2-005e60b90f7f",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2487.70.105"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703359963136,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4829181,
"uuid" : "c5e5acb6-9e44-3aa3-bd21-0a5b4a2eee5e",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "2602"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703538659328,
"CFBundleShortVersionString" : "2.1.1",
"CFBundleIdentifier" : "com.apple.HIToolbox",
"size" : 2732020,
"uuid" : "2aa738bf-9f72-3227-8bba-7eae7b9f080b",
"path" : "\/System\/Library\/Frameworks\/Carbon.framework\/Versions\/A\/Frameworks\/HIToolbox.framework\/Versions\/A\/HIToolbox",
"name" : "HIToolbox"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703355822080,
"size" : 591904,
"uuid" : "18f658dd-20f3-324d-b7ac-8a9c60b574b3",
"path" : "\/usr\/lib\/dyld",
"name" : "dyld"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703358705664,
"size" : 503796,
"uuid" : "69eca28c-bfb7-35bf-ad4f-1bece712d239",
"path" : "\/usr\/lib\/libc++.1.dylib",
"name" : "libc++.1.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703416070144,
"CFBundleShortVersionString" : "2.0.2",
"CFBundleIdentifier" : "com.apple.framework.IOKit",
"size" : 802816,
"uuid" : "e9d77063-8c99-3bd6-b5f4-f8c4cd890561",
"path" : "\/System\/Library\/Frameworks\/IOKit.framework\/Versions\/A\/IOKit",
"name" : "IOKit"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703533486080,
"CFBundleShortVersionString" : "481.40.2",
"CFBundleIdentifier" : "com.apple.IOAccelerator",
"size" : 36856,
"uuid" : "05e3c7a8-a0f2-3c4f-b064-2168108aa254",
"path" : "\/System\/Library\/PrivateFrameworks\/IOAccelerator.framework\/Versions\/A\/IOAccelerator",
"name" : "IOAccelerator",
"CFBundleVersion" : "481.40.2"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712451092480,
"CFBundleShortVersionString" : "5.4",
"CFBundleIdentifier" : "com.apple.opencl",
"size" : 360448,
"uuid" : "28c42c8a-f074-3501-8d74-1565dc1f474a",
"path" : "\/System\/Library\/Frameworks\/OpenCL.framework\/Versions\/A\/OpenCL",
"name" : "OpenCL",
"CFBundleVersion" : "5.4"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703357845504,
"size" : 290802,
"uuid" : "ffb968b0-807c-38bf-ae61-50a96c8d310c",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
"name" : "libdispatch.dylib"
}
],
"sharedCache" : {
"base" : 140703355125760,
"size" : 25769803776,
"uuid" : "b8509d0f-c366-3716-9a03-efa00b40318a"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.3G resident=0K(0%) swapped_out_or_unallocated=1.3G(100%)\nWritable regions: Total=3.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 184K 14 \nColorSync 248K 30 \nCoreAnimation 952K 111 \nCoreGraphics 24K 4 \nCoreUI image data 4540K 34 \nDispatch continuations 64.0M 1 \nFoundation 40K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 2.4G 2928 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenCL 4732K 82 \nOpenCL (reserved) 220K 8 reserved VM address space (unallocated)\nOpenGL GLSL 384K 4 \nSTACK GUARD 180K 45 \nStack 158.4M 46 \nStack Guard 56.0M 1 \nVM_ALLOCATE 380.6M 492 \nVM_ALLOCATE (reserved) 128.0M 3 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 48.3M 899 \n__DATA_CONST 53.2M 463 \n__DATA_DIRTY 1842K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 226.6M 254 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2201K 2 \n__TEXT 1.1G 899 \ndyld private memory 128K 2 \nmapped file 229.5M 63 \nshared memory 3000K 31 \n=========== ======= ======= \nTOTAL 5.0G 6670 \nTOTAL, minus reserved VM space 4.9G 6670 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "0000b9c5cd04db741ec21b3ff28b266582be57d3",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
},
"deploymentId" : 240000008
},
{
"rolloutId" : "648c94d4ebdf9e3e398fa708",
"factorPackIds" : {
"SIRI_UNDERSTANDING_NL_OVERRIDES" : "65a8104b6712a43e7922cab8"
},
"deploymentId" : 240000171
}
],
"experiments" : [
{
"treatmentId" : "28060e10-d4e5-4163-aa2b-d8bd088d5cbf",
"experimentId" : "6685b283afc7c17197d69eec",
"deploymentId" : 400000007
}
]
}
}
===== 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/victoriaxu/Downloads/cryosparc_P1_J3811_000_volume_map.mrc
Opened cryosparc_P1_J3811_000_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.931, shown at level 0.267, step 4, values float32
> volume #1 level 0.1915
> volume #1 step 1
> volume #1 level 0.1331
> ui tool show "Side View"
> volume #1 level 0.1961
> volume #1 level 0.2148
> volume #1 level 0.2323
> lighting simple
> volume #1 level 0.2568
> open /Users/victoriaxu/Downloads/pentamer_fittedinJ3787_005.cif
Chain information for pentamer_fittedinJ3787_005.cif #2
---
Chain | Description
F G H I J | No description available
T U e h i | No description available
> close #1
> set bgColor white
> open /Users/victoriaxu/Downloads/cryosparc_P1_J3787_005_volume_map.mrc
Opened cryosparc_P1_J3787_005_volume_map.mrc as #1, grid size 588,588,588,
pixel 0.931, shown at level 0.4, step 4, values float32
> style stick
Changed 63680 atom styles
> color bychain
> color byhetero
> show cartoons
> hide atoms
> volume #1 step 1
> vop flip #1
Opened cryosparc_P1_J3787_005_volume_map.mrc z flip as #3, grid size
588,588,588, pixel 0.931, shown at step 1, values float32
> close #1
> transparency 50
> transparency 0
> transparency 50
> ui tool show ISOLDE
> 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
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #2 to IUPAC-IUB
standards.
Chain information for pentamer_fittedinJ3787_005.cif
---
Chain | Description
1.2/F 1.2/G 1.2/H 1.2/I 1.2/J | No description available
1.2/T 1.2/U 1.2/e 1.2/h 1.2/i | No description available
> clipper associate #3 toModel #1
Opened cryosparc_P1_J3787_005_volume_map.mrc z flip as #1.1.1.1, grid size
588,588,588, pixel 0.931, shown at step 1, values float32
> isolde sim start
> /U:487-510,528-542,544-546,550-551,553-564,574-578,596-597,599
ISOLDE: started sim
> select clear
> volume #1.1.1.1 level 0.654
> isolde pepflip /U:503
> isolde pepflip /U:504
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /T:489-509,539,555-560
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /T:520,522
ISOLDE: started sim
> isolde cisflip /T:520
> isolde cisflip /T:521
> isolde pepflip /T:524
> isolde pepflip /T:525
> isolde pepflip #!1.2/T:521
> isolde pepflip /T:524
> isolde pepflip /T:525
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /T:525
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.4565
> isolde sim start /T:707-708,711
ISOLDE: started sim
> volume #1.1.1.1 level 0.3797
> isolde pepflip /T:707
> isolde pepflip /T:708
> isolde pepflip /T:713
> isolde pepflip /T:711
> volume #1.1.1.1 level 0.4113
> volume #1.1.1.1 level 0.2034
> volume #1.1.1.1 level 0.3706
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde add ligand ADP
Deleted the following atoms from residue ADP T2000: HOA2, HOB2, HOB3
> isolde sim start /T:2000
Loading residue template for ADP from internal database
ISOLDE: started sim
> volume #1.1.1.1 level 0.4746
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.5823
> isolde add ligand MG
> isolde sim start /T:2000-2001
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.3838
> isolde sim start /U:266
ISOLDE: started sim
> volume #1.1.1.1 level 0.2444
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.7806
> volume #1.1.1.1 level 0.6373
> isolde sim start /U:708,712
ISOLDE: started sim
> volume #1.1.1.1 level 0.389
> isolde pepflip /U:711
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /e:266,268
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /e:499,503
ISOLDE: started sim
> isolde pepflip /e:499
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /e:521
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /e:708
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> volume #1.1.1.1 level 0.5256
> isolde add ligand ADP
Deleted the following atoms from residue ADP e2000: HOA2, HOB3, HOB2
> isolde sim start /e:705-711,2000
ISOLDE: started sim
===== 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-22.5.11
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0)
OS Loader Version: 580.140.1~8
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 4 days, 9 hours, 4 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
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: No
Connection Type: Internal
MateView:
Resolution: 3840 x 2560
UI Looks like: 1920 x 1280 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number:
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
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
MolecularDynamicsViewer: 1.6
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 , 6 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 , 6 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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