![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 9 months ago
Closed 9 months ago
#16786 closed defect (nonchimerax)
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-15.2-x86_64-i386-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics.
Fatal Python error: Aborted
Current thread 0x00007ff859a614c0 (most recent call first):
File "/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py", line 561 in swap_buffers
File "/Applications/ChimeraX-1.9.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-1.9.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-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 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, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast (total: 56)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,2",
"coalitionID" : 7834,
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"build" : "24C101",
"releaseType" : "User"
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"captureTime" : "2025-02-05 13:28:12.7556 +0100",
"codeSigningMonitor" : 0,
"incident" : "BAC1D34E-11BA-454A-BBE1-72F1261C3707",
"pid" : 65868,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-01-31 15:59:48.5971 +0100",
"procStartAbsTime" : 549637926237991,
"procExitAbsTime" : 622373617124014,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2D1D3C45-E2CD-50DC-B3E4-890A9DF5387C","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C9E08316-F481-AE51-0088-DBB74F890D4B",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "5FDB8C10-361E-4257-BC18-F08FBBA49A4B",
"wakeTime" : 4432,
"bridgeVersion" : {"build":"22P2093","train":"9.2"},
"sleepWakeUUID" : "F7F46CA9-951F-40E2-A0BD-D0B8C89AEFDC",
"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":65868},
"ktriageinfo" : "VM - (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"],
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"CFBundleIdentifier" : "com.apple.Foundation",
"size" : 14884852,
"uuid" : "80444dda-74a7-353b-a8d4-3e3a05d275d6",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "3208"
}
],
"sharedCache" : {
"base" : 140703506911232,
"size" : 25769803776,
"uuid" : "d71b956e-cf0a-3cfa-9def-2bfdfda32722"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=2.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2384K 2 \nCG image 820K 104 \nCG raster data 8K 1 \nColorSync 260K 33 \nCoreAnimation 1816K 157 \nCoreGraphics 32K 7 \nCoreUI image data 5436K 53 \nFoundation 52K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 1.6G 1096 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 120K 30 \nStack 188.2M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 372.8M 347 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 40.8M 1084 \n__DATA_CONST 102.5M 1000 \n__DATA_DIRTY 2570K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5176K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 215.3M 154 \n__OBJC_RO 76.9M 1 \n__OBJC_RW 2373K 2 \n__TEXT 1.3G 1100 \n__TPRO_CONST 272K 2 \ndyld private memory 40K 2 \nmapped file 573.3M 89 \nowned unmapped memory 194.2M 1 \nshared memory 3532K 33 \n=========== ======= ======= \nTOTAL 4.8G 5707 \nTOTAL, minus reserved VM space 4.7G 5707 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "70f48e7c96000397af6cb23ae82c233a3466ab11",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "67181b10c68c361a728c7cfa",
"factorPackIds" : {
},
"deploymentId" : 240000004
},
{
"rolloutId" : "642da32dea3b2418c750f848",
"factorPackIds" : {
"VISUAL_INTELLIGENCE_VICTORIA" : "66d8b2f77cd4b62688efd2cf"
},
"deploymentId" : 240000004
}
],
"experiments" : [
{
"treatmentId" : "be4e6d84-1e65-44cd-b2b5-85110e02c3e5",
"experimentId" : "66d9e11556f9247c8bf41f49",
"deploymentId" : 400000003
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/lau/Downloads/4xTre6P_TPS1_wt/pred.rank_4.cif
Summary of feedback from opening
/Users/lau/Downloads/4xTre6P_TPS1_wt/pred.rank_4.cif
---
warnings | Unable to fetch template for 'LIG1': will connect using distance criteria
Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
pred.rank_4.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_4.cif #1
---
Chain | Description
E | Entity E
Non-standard residues in pred.rank_4.cif #1
---
LIG1 — (LIG1)
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color pred.rank_4.cif by residue attribute pLDDT_score
Computing secondary structure
> close
> open /Users/lau/Downloads/4xTre6P_TPS1_wt/4xTre6P_TPS1_Chai1_0.cif
Summary of feedback from opening
/Users/lau/Downloads/4xTre6P_TPS1_wt/4xTre6P_TPS1_Chai1_0.cif
---
warnings | Unable to fetch template for 'LIG1': will connect using distance criteria
Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
4xTre6P_TPS1_Chai1_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for 4xTre6P_TPS1_Chai1_0.cif #1
---
Chain | Description
E | Entity E
Non-standard residues in 4xTre6P_TPS1_Chai1_0.cif #1
---
LIG1 — (LIG1)
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color 4xTre6P_TPS1_Chai1_0.cif by residue attribute pLDDT_score
Computing secondary structure
> open /Users/lau/Downloads/TPS1_Chai/TPS1_Chai1_0.cif
TPS1_Chai1_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for TPS1_Chai1_0.cif #2
---
Chain | Description
A | Entity A
Color TPS1_Chai1_0.cif by residue attribute pLDDT_score
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #1/E to #2/A pairing ss
Computing secondary structure
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TPS1_Chai1_0.cif, chain A (#2) with 4xTre6P_TPS1_Chai1_0.cif, chain
E (#1), sequence alignment score = 4582.8
RMSD between 462 pruned atom pairs is 0.507 angstroms; (across all 942 pairs:
23.831)
> open /Users/lau/Downloads/TPS1_2xT6P/2xTre6P_TPS1_Chai1_0.cif
Summary of feedback from opening
/Users/lau/Downloads/TPS1_2xT6P/2xTre6P_TPS1_Chai1_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
2xTre6P_TPS1_Chai1_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for 2xTre6P_TPS1_Chai1_0.cif #3
---
Chain | Description
A | Entity A
Non-standard residues in 2xTre6P_TPS1_Chai1_0.cif #3
---
LIG2 — (LIG2)
LIG3 — (LIG3)
Color 2xTre6P_TPS1_Chai1_0.cif by residue attribute pLDDT_score
Computing secondary structure
> open /Users/lau/Downloads/TPS1_1xT6P/1xTre6P_TPS1_Chai1_0.cif
Summary of feedback from opening
/Users/lau/Downloads/TPS1_1xT6P/1xTre6P_TPS1_Chai1_0.cif
---
warning | Unable to fetch template for 'LIG2': will connect using distance criteria
1xTre6P_TPS1_Chai1_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for 1xTre6P_TPS1_Chai1_0.cif #4
---
Chain | Description
A | Entity A
Non-standard residues in 1xTre6P_TPS1_Chai1_0.cif #4
---
LIG2 — (LIG2)
Color 1xTre6P_TPS1_Chai1_0.cif by residue attribute pLDDT_score
Computing secondary structure
> open /Users/lau/Downloads/TPS1_3xT6P/3xTre6P_TPS1_Chai1_0.cif
Summary of feedback from opening
/Users/lau/Downloads/TPS1_3xT6P/3xTre6P_TPS1_Chai1_0.cif
---
warnings | Unable to fetch template for 'LIG2': will connect using distance criteria
Unable to fetch template for 'LIG3': will connect using distance criteria
Unable to fetch template for 'LIG4': will connect using distance criteria
3xTre6P_TPS1_Chai1_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for 3xTre6P_TPS1_Chai1_0.cif #5
---
Chain | Description
A | Entity A
Non-standard residues in 3xTre6P_TPS1_Chai1_0.cif #5
---
LIG2 — (LIG2)
LIG3 — (LIG3)
LIG4 — (LIG4)
Color 3xTre6P_TPS1_Chai1_0.cif by residue attribute pLDDT_score
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #3-5 to #2/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TPS1_Chai1_0.cif, chain A (#2) with 2xTre6P_TPS1_Chai1_0.cif, chain
A (#3), sequence alignment score = 4690.8
RMSD between 484 pruned atom pairs is 0.693 angstroms; (across all 942 pairs:
12.504)
Matchmaker TPS1_Chai1_0.cif, chain A (#2) with 1xTre6P_TPS1_Chai1_0.cif, chain
A (#4), sequence alignment score = 4635
RMSD between 476 pruned atom pairs is 0.527 angstroms; (across all 942 pairs:
24.891)
Matchmaker TPS1_Chai1_0.cif, chain A (#2) with 3xTre6P_TPS1_Chai1_0.cif, chain
A (#5), sequence alignment score = 4662.6
RMSD between 482 pruned atom pairs is 0.590 angstroms; (across all 942 pairs:
25.335)
> select #2/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #2/A:1-10
74 atoms, 75 bonds, 10 residues, 1 model selected
> select #2/A:1-88
700 atoms, 708 bonds, 88 residues, 1 model selected
> select #2/A:900-942
329 atoms, 334 bonds, 43 residues, 1 model selected
> color sel yelllow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> colour sel yelllow
> color sel yelllow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> colour sel navy
> hide #3 models
> hide #4 models
> hide #5 models
> hide #1 models
> select clear
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #4 models
> hide #4 models
> show #3 models
> hide #3 models
> show #5 models
> hide #5 models
> show #1 models
> hide #1 models
> show #4 models
> hide #4 models
> show #4 models
> hide #2 models
> show #2 models
> hide #2 models
> show #1 models
> hide #1 models
> show #2 models
> hide #4 models
> show #3 models
> hide #3 models
> show #5 models
> hide #2 models
> show #1 models
> hide #5 models
> show #2 models
> hide #2 models
> show #5 models
> hide #1 models
> show #3 models
> show #2 models
> show #4 models
> hide #3 models
> hide #2 models
> show #1 models
> show #3 models
> hide #3 models
> show #2 models
> show #3 models
> hide #4 models
> hide #1 models
> hide #2 models
> show #4 models
> hide #5 models
> show #2 models
> hide #3 models
> show #1 models
> hide #1 models
> show #1 models
> show #3 models
> show #5 models
> hide #5 models
> hide #2 models
> hide #1 models
> hide #4 models
> hide #3 models
> show #4 models
> select #4/A:1-88
700 atoms, 708 bonds, 88 residues, 1 model selected
> color sel yellow
> show #2 models
> select #2/A:1-88
700 atoms, 708 bonds, 88 residues, 1 model selected
> color sel yellow
> hide #4 models
> show #4 models
> hide #2 models
> show #2 models
> hide #2 models
> ui tool show Contacts
> select #4/B
27 atoms, 28 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel saveFile /Users/lau/Desktop/,mn,mn, resSeparation 10 interModel
> false intraMol false color #07ffff dashes 5 radius 0.105 reveal true
46 contacts
> hide #!4 models
> show #3 models
> open /Users/lau/Downloads/ligand-1-protein-1-protein-1/pred.rank_0.cif
Summary of feedback from opening
/Users/lau/Downloads/ligand-1-protein-1-protein-1/pred.rank_0.cif
---
warning | Unable to fetch template for 'LIG1': will connect using distance criteria
pred.rank_0.cif title:
Chai-1 predicted structure [more info...]
Chain information for pred.rank_0.cif #6
---
Chain | Description
B | Entity B
C | Entity C
Non-standard residues in pred.rank_0.cif #6
---
LIG1 — (LIG1)
Color pred.rank_0.cif by residue attribute pLDDT_score
Computing secondary structure
> hide #3 models
> select #6/B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> lighting simple
> color sel yellow
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select #6/A
27 atoms, 28 bonds, 1 residue, 1 model selected
> color sel red
> hide sel atoms
> show sel atoms
> select #6/C
4301 atoms, 4396 bonds, 535 residues, 1 model selected
> select #6/C:175
6 atoms, 5 bonds, 1 residue, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> select #6/C:175,63,64,65
25 atoms, 23 bonds, 4 residues, 1 model selected
> select #6/C:175,63,64,65
25 atoms, 23 bonds, 4 residues, 1 model selected
> select #6/C:175,63-73
89 atoms, 88 bonds, 12 residues, 1 model selected
Unsupported scale factor (0.000000) detected on Display0
> show sel atoms
> hide sel atoms
Unsupported scale factor (0.000000) detected on Display0
> show #!4 models
> ui tool show Matchmaker
Unsupported scale factor (0.000000) detected on Display2
> matchmaker #!6 to #2/A pairing bs
Computing secondary structure
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker TPS1_Chai1_0.cif, chain A (#2) with pred.rank_0.cif, chain B (#6),
sequence alignment score = 4611.6
RMSD between 460 pruned atom pairs is 0.568 angstroms; (across all 942 pairs:
33.738)
> hide #!4 models
> show #2 models
> show #!4 models
> show #1 models
> show #3 models
> show #5 models
> hide #4.1 models
> hide #5 models
> hide #1 models
> hide #3 models
> hide #!6 models
> show #!6 models
> hide #!4 models
> hide #2 models
> ui tool show Contacts
> contacts resSeparation 10 interModel false intraMol false color #ff5518
> dashes 5 radius 0.105 reveal true
989 contacts
Unsupported scale factor (0.000000) detected on Display2
> ui tool show Contacts
> contacts saveFile /Users/lau/Desktop/TPS1-T6P-KIN10 resSeparation 10
> interModel false intraMol false color #ff5518 dashes 5 radius 0.105 reveal
> true
989 contacts
> hide #7 models
> show #7 models
> select #6/A
27 atoms, 28 bonds, 1 residue, 1 model selected
> color sel blue
> select clear
> surface #6-7
> surface style mesh
> transparency #6-7 70
> hide #!6 surfaces
> graphics silhouettes true
> surface style dot
> lighting shadows true
> graphics silhouettes false
> lighting shadows false
> lighting full
> nucleotides #!6 tube/slab shape box
> lighting soft
> lighting full
> lighting soft
> lighting simple
> seelct #6/B
Unknown command: seelct #6/B
> select #6/B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> seelct clear
Unknown command: seelct clear
> select clear
> select #6/A
27 atoms, 28 bonds, 1 residue, 1 model selected
> select #6/B
7461 atoms, 7623 bonds, 942 residues, 1 model selected
> select #6/B:1-30
249 atoms, 252 bonds, 30 residues, 1 model selected
> select #6/B:1-35
294 atoms, 297 bonds, 35 residues, 1 model selected
> select #6/B:10-35
226 atoms, 227 bonds, 26 residues, 1 model selected
> hide #!6 models
> hide #7 models
> show #!4 models
Unsupported scale factor (0.000000) detected on Display0
Unsupported scale factor (0.000000) detected on Display2
> show #!6 models
> hide #!4 models
> show #7 models
> hide #7 models
> select add #6.2
4527 atoms, 227 bonds, 561 residues, 2 models selected
> select subtract #6.2
226 atoms, 227 bonds, 26 residues, 3 models selected
> select subtract #6.1
1 model selected
> hide #6.1 models
> hide #6.2 models
> open /Users/lau/Downloads/fold_kin10_tps1/fold_kin10_tps1_model_0.cif
Chain information for fold_kin10_tps1_model_0.cif #8
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #!6 models
> show #!6 models
> ui tool show Matchmaker
> matchmaker #!6 to #8
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker fold_kin10_tps1_model_0.cif, chain A (#8) with pred.rank_0.cif,
chain B (#6), sequence alignment score = 4532.4
RMSD between 443 pruned atom pairs is 0.707 angstroms; (across all 942 pairs:
43.808)
> select #8/B:10-35
191 atoms, 192 bonds, 26 residues, 1 model selected
> hide #!6 models
> select #8/B
4302 atoms, 4397 bonds, 535 residues, 1 model selected
> color sel white
> ui tool show Contacts
> contacts sel resSeparation 10 interModel false intraMol false color #ff5518
> dashes 5 radius 0.105 reveal true
256 contacts
> select #8/A:1-30
249 atoms, 252 bonds, 30 residues, 1 model selected
> show #!6 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!6 models
> show #!8 models
Unsupported scale factor (0.000000) detected on Display2
Unsupported scale factor (0.000000) detected on Display0
> hide #!8 models
> show #!8 models
> hide #!8 models
> select add #8
11764 atoms, 12021 bonds, 256 pseudobonds, 1477 residues, 2 models selected
> select subtract #8
Nothing selected
> show #!8 models
> select add #8
11764 atoms, 12021 bonds, 256 pseudobonds, 1477 residues, 2 models selected
> select subtract #8
Nothing selected
> select add #8
11764 atoms, 12021 bonds, 256 pseudobonds, 1477 residues, 2 models selected
> hide #!8 models
> select subtract #8
Nothing selected
> show #2 models
> show #!4 models
> hide #2 models
> show #!6 models
> hide #!4 models
> hide #!6 models
> show #!8 models
> hide #8.1 models
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-23.0.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2.3 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: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.12093.0.0,0)
OS Loader Version: 582~2898
Software:
System Software Overview:
System Version: macOS 15.2 (24C101)
Kernel Version: Darwin 24.2.0
Time since boot: 22 days, 22 hours, 8 minutes
Graphics/Displays:
Intel Iris Plus Graphics 655:
Chipset Model: Intel Iris Plus Graphics 655
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea5
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: No
Connection Type: Internal
DELL P2425:
Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
UI Looks like: 1920 x 1200 @ 59.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 1CRC304
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: Thunderbolt/DisplayPort
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
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: 2.3
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: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
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: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
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: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
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-MutationScores: 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: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
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: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
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: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
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: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
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: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
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: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 9 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 , 9 months ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
The ChimeraX Report a Bug dialog that you used gave the following info about this crash, shown in red.
"This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics."
Unfortunately Apple's Intel graphics drivers are not very stable. There is nothing we can do to fix that. Apple's newer machines using Apple Silicon graphics are very stable, with almost no graphics crashes reported in the past 4 years.
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Reported by Laura Lamelas