![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9833 closed defect (nonchimerax)
Graphics crash, macOS 13.5.2, Intel Iris Plus Graphics
| 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-13.5.2-x86_64-i386-64bit
ChimeraX Version: 1.7.dev202307220101 (2023-07-22 01:01:24 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Current thread 0x00007ff852552700 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 2730 in draw_elements
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1741 in draw
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 841 in _draw_geometry
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 776 in draw_self
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 769 in draw
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1556 in _draw_multiple
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1543 in draw_opaque
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 288 in render
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py", line 113 in _redraw
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 138 in invoke
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 237 in _activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 206 in activate
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 382 in activate_trigger
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 89 in draw_new_frame
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 in init
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1044 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, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 53)
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{
"uptime" : 250000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 21144,
"osVersion" : {
"train" : "macOS 13.5.2",
"build" : "22G91",
"releaseType" : "User"
},
"captureTime" : "2023-09-25 00:04:11.3426 +0800",
"incident" : "BEC2FF6F-D597-446A-91DA-CD7FBD0E4BEC",
"pid" : 31486,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-09-24 23:33:23.4708 +0800",
"procStartAbsTime" : 255173811227819,
"procExitAbsTime" : 257021704343914,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"316A5C6F-43A2-511A-9D7E-AF302FFE82C2","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "AF09E589-6246-163F-86AC-26EC9ECFAF8A",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 5079,
"bridgeVersion" : {"build":"20P6072","train":"7.6"},
"sleepWakeUUID" : "FFF178A4-F651-4E5D-ADF4-D9CE10D58C3F",
"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":31486},
"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,
"threads" : 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"uuid" : "ae00e899-7993-3ab7-a959-d803e7c88dcf",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.70.136"
}
],
"sharedCache" : {
"base" : 140703374512128,
"size" : 21474836480,
"uuid" : "9e62ff5d-f36e-3c12-9277-95f6a085513e"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=3.4G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=3.4G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 2880K 8 \nCG image 128K 8 \nColorSync 268K 30 \nCoreAnimation 260K 12 \nCoreGraphics 16K 3 \nCoreServices 624K 2 \nCoreUI image data 3080K 22 \nFoundation 40K 2 \nIOAccelerator 156.7M 209 \nIOKit 15.8M 19 \nIOSurface 114.3M 49 \nKernel Alloc Once 1384K 5 \nMALLOC 1.9G 172 \nMALLOC guard page 48K 11 \nMALLOC_MEDIUM (reserved) 624.0M 8 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 88K 22 \nStack 146.7M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 228.6M 126 \n__CTF 824 1 \n__DATA 48.5M 773 \n__DATA_CONST 50.0M 465 \n__DATA_DIRTY 1850K 235 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 202.3M 146 \n__OBJC_RO 66.3M 1 \n__OBJC_RW 2013K 2 \n__TEXT 969.1M 779 \ndyld private memory 292K 4 \nmapped file 223.2M 57 \nshared memory 59.3M 144 \n=========== ======= ======= \nTOTAL 5.0G 3353 \nTOTAL, minus reserved VM space 4.2G 3353 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "f8f8d273ee71c202296cc08b849c35bf80acc5fe",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "61675b89201f677a9a4cbd65",
"factorPackIds" : {
"HEALTH_FEATURE_AVAILABILITY" : "64d14f3e1008ca2fac17a163"
},
"deploymentId" : 240000064
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
}
],
"experiments" : [
{
"treatmentId" : "3a3cf641-8471-4e4e-9ad4-81d0ede970fd",
"experimentId" : "64a84dae90d82611a0bd7d3d",
"deploymentId" : 400000004
},
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000017
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.dev202307220101 (2023-07-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/mi/Documents/000-download papers/5btc.pdb"
5btc.pdb title:
Crystal structure of A topoisomerase II complex [more info...]
Chain information for 5btc.pdb #1
---
Chain | Description | UniProt
A C | DNA gyrase subunit A | GYRA_MYCTU 2-500
B D | DNA gyrase subunit B | GYRB_MYCTU 426-675
E H | DNA substrate 24-mer ggtcatgaatgactatgcacgtaa |
F G | DNA substrate 24-mer ttacgtgcatagtcattcatgacc |
Non-standard residues in 5btc.pdb #1
---
CPF —
1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic
acid (ciprofloxacin)
MG — magnesium ion
> hide #1.1 models
> hide #1.2 models
> open 5btc fromDatabase rcsb_bio maxAssemblies 1
Summary of feedback from opening 5btc fetched from rcsb_bio
---
notes | Fetching compressed 5btc bioassembly 1 from
https://files.rcsb.org/download/5btc-assembly1.cif
Fetching CCD CPF from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CPF/CPF.cif
5btc bioassembly 1 title:
Crystal structure of a topoisomerase II complex [more info...]
Chain information for 5btc bioassembly 1 #2
---
Chain | Description
A C | DNA gyrase subunit A
B D | DNA gyrase subunit B
E H | DNA substrate 24-mer GGTCATGAATGACTATGCACGTAA
F G | DNA substrate 24-mer TTACGTGCATAGTCATTCATGACC
Non-standard residues in 5btc bioassembly 1 #2
---
CPF —
1-cyclopropyl-6-fluoro-4-oxo-7-piperazin-1-yl-1,4-dihydroquinoline-3-carboxylic
acid (ciprofloxacin)
MG — magnesium ion
Opened 1 biological assemblies for 5btc
> hide #!1 models
> hide :gol
> hide solvent
> hide protein
> select clear
> hide DNA
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> coulombic protein
The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:
5btc bioassembly 1 #2/B VAL 675 OXT
5btc bioassembly 1 #2/D VAL 675 OXT
5btc.pdb #1/D VAL 675 OXT
5btc.pdb #1/B VAL 675 OXT
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp9twjngp3/ante.in.mol2 -fi
mol2 -o
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp9twjngp3/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(PTR) ``
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR) ``
(PTR) `Info: Finished reading file
(/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp9twjngp3/ante.in.mol2);
atoms read (36), bonds read (36).`
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR) ``
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PTR) `Info: Total number of electrons: 166; net charge: -2`
(PTR) ``
(PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR) ``
Charges for residue PTR determined
Assigning partial charges to residue PTR (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpuyk4cs93/ante.in.mol2 -fi
mol2 -o
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpuyk4cs93/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(PTR) ``
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR) ``
(PTR) `Info: Finished reading file
(/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpuyk4cs93/ante.in.mol2);
atoms read (37), bonds read (37).`
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR) ``
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PTR) `Info: Total number of electrons: 166; net charge: -1`
(PTR) ``
(PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR) ``
Charges for residue PTR determined
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue PTR (net charge -1) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp2i4_iu5w/ante.in.mol2 -fi
mol2 -o
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp2i4_iu5w/ante.out.mol2 -fo
mol2 -c bcc -nc -1 -j 5 -s 2 -dr n
(PTR) ``
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR) ``
(PTR) `Info: Finished reading file
(/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmp2i4_iu5w/ante.in.mol2);
atoms read (37), bonds read (37).`
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR) ``
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PTR) `Info: Total number of electrons: 166; net charge: -1`
(PTR) ``
(PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR) ``
Charges for residue PTR determined
Assigning partial charges to residue PTR (net charge -2) with am1-bcc method
Running ANTECHAMBER command:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpqxj4lvr3/ante.in.mol2 -fi
mol2 -o
/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpqxj4lvr3/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n
(PTR) ``
(PTR) `Welcome to antechamber 20.0: molecular input file processor.`
(PTR) ``
(PTR) `Info: Finished reading file
(/var/folders/hc/vp0c3h0x39v6h6v2dwkfkzsr0000gn/T/tmpqxj4lvr3/ante.in.mol2);
atoms read (36), bonds read (36).`
(PTR) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(PTR) ``
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(PTR) `Info: Total number of electrons: 166; net charge: -2`
(PTR) ``
(PTR) `Running: /Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(PTR) ``
(PTR) `Running:
/Applications/ChimeraX_Daily.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(PTR) ``
Charges for residue PTR determined
Coulombic values for 5btc.pdb_A SES surface #1.3: minimum, -20.85, mean -1.74,
maximum 14.01
Coulombic values for 5btc.pdb_B SES surface #1.4: minimum, -20.08, mean 0.02,
maximum 14.55
Coulombic values for 5btc.pdb_C SES surface #1.5: minimum, -22.98, mean -1.77,
maximum 13.69
Coulombic values for 5btc.pdb_D SES surface #1.6: minimum, -20.10, mean 0.10,
maximum 19.59
Coulombic values for 5btc bioassembly 1_A SES surface #2.2: minimum, -20.85,
mean -1.74, maximum 14.01
Coulombic values for 5btc bioassembly 1_B SES surface #2.3: minimum, -20.08,
mean 0.02, maximum 14.55
Coulombic values for 5btc bioassembly 1_C SES surface #2.4: minimum, -22.98,
mean -1.77, maximum 13.69
Coulombic values for 5btc bioassembly 1_D SES surface #2.5: minimum, -20.10,
mean 0.10, maximum 19.59
> color nucleic tan
> cartoon style nucleic xsection round width 1.5 thickness 1.5
> nucleotides stubs
> nucleotides #!2 atoms
> style nucleic & #!2 stick
Changed 2469 atom styles
> nucleotides #!2 atoms
> style nucleic & #!2 stick
Changed 2469 atom styles
> style #!2 stick
Changed 25950 atom styles
> nucleotides #!2 fill
> style nucleic & #!2 stick
Changed 2469 atom styles
> lighting simple
> lighting shadows true
> lighting shadows false
> lighting flat
> ui tool show "Side View"
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> lighting shadows true intensity 0.5
> view orient
> nucleotides stubs
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.dev202307220101 (2023-07-22)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> ui tool show Registration
OpenGL version: 4.1 INTEL-20.6.4
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.5.1, Qt 6.5.1
Qt runtime version: 6.5.1
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1968.140.7.0.0 (iBridge: 20.16.6072.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.5.2 (22G91)
Kernel Version: Darwin 22.6.0
Time since boot: 11 minutes, 4 seconds
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: Yes
Connection Type: Internal
S24E360:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.2.0
ChimeraX-AddCharge: 1.5.11
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.46.1
ChimeraX-AtomicLibrary: 10.0.8
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.4
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202307220101
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.2
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: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.1.1
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.9
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 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: 1.31.1
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.1.0
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.41.1
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.9.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.38
imagecodecs: 2023.7.10
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.7
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.3.1
jupyterlab-widgets: 3.0.8
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 10.0.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.9.1
prompt-toolkit: 3.0.39
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.5.1
PyQt6-Qt6: 6.5.1
PyQt6-sip: 13.5.1
PyQt6-WebEngine-commercial: 6.5.0
PyQt6-WebEngine-Qt6: 6.5.1
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.1.0
qtconsole: 5.4.3
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
traitlets: 5.9.0
typing-extensions: 4.7.1
tzdata: 2023.3
urllib3: 2.0.4
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.8
Change History (2)
comment:1 by , 2 years 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 , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.5.2, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.