![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9893 closed defect (nonchimerax)
Graphics crash, macOS 13.2.1, Intel Iris Plus Graphics 645
| 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-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
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{
"uptime" : 350000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
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"captureTime" : "2023-10-03 09:41:49.8588 +1300",
"incident" : "85CDE376-DABB-47BE-9F8B-2E9C87367410",
"pid" : 93706,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-03 09:40:00.2199 +1300",
"procStartAbsTime" : 352636537973103,
"procExitAbsTime" : 352746167286397,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
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"sleepWakeUUID" : "4DF64A9B-D739-4B13-B968-CA57873216AF",
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"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
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"path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
"name" : "libGPUSupportMercury.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712030642176,
"CFBundleShortVersionString" : "20.2.50",
"CFBundleIdentifier" : "com.apple.driver.AppleIntelKBLGraphicsGLDriver",
"size" : 16039936,
"uuid" : "3c704f18-4e36-3228-bf8a-7647f6ed24fb",
"path" : "\/System\/Library\/Extensions\/AppleIntelKBLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelKBLGraphicsGLDriver",
"name" : "AppleIntelKBLGraphicsGLDriver",
"CFBundleVersion" : "20.0.2"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712168296448,
"size" : 1613816,
"uuid" : "5659457d-2e03-3826-b003-c422b503973b",
"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Resources\/GLEngine.bundle\/GLEngine",
"name" : "GLEngine"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703473655808,
"size" : 24544,
"uuid" : "bb553223-8d2b-3662-a6db-739b0772fd89",
"path" : "\/usr\/lib\/libffi.dylib",
"name" : "libffi.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 5095100416,
"size" : 174571520,
"uuid" : "473ca65c-6149-3bfa-a88b-95ac735bcd3b",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtWebEngineCore.framework\/Versions\/A\/QtWebEngineCore",
"name" : "QtWebEngineCore"
},
{
"source" : "P",
"arch" : "x86_64h",
"base" : 140703216779264,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.CoreFoundation",
"size" : 4825072,
"uuid" : "c2615780-0140-315c-a455-7e03bb22d3d6",
"path" : "\/System\/Library\/Frameworks\/CoreFoundation.framework\/Versions\/A\/CoreFoundation",
"name" : "CoreFoundation",
"CFBundleVersion" : "1953.300"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703268749312,
"CFBundleShortVersionString" : "6.9",
"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16814067,
"uuid" : "540cedfd-5a35-3f35-8953-dcb7c4834eb5",
"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
"CFBundleVersion" : "2299.40.118"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4561915904,
"size" : 64028672,
"uuid" : "24c9d5c5-4854-3af4-9550-cb0204044dfa",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib",
"name" : "libopenblas64_.0.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4553793536,
"size" : 5210112,
"uuid" : "6238782e-d1aa-3245-81ef-2925bf1a4c96",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt6\/Qt6\/lib\/QtCore.framework\/Versions\/A\/QtCore",
"name" : "QtCore"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 4453007360,
"CFBundleShortVersionString" : "3.9.11, (c) 2001-2021 Python Software Foundation.",
"CFBundleIdentifier" : "org.python.python",
"size" : 2527232,
"uuid" : "ef9cc1f4-5991-3213-9a9e-e68c578b6c1b",
"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/Python",
"name" : "Python",
"CFBundleVersion" : "3.9.11"
}
],
"sharedCache" : {
"base" : 140703212417024,
"size" : 21474836480,
"uuid" : "57815a20-af2c-3b56-9006-23abde7962b0"
},
"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=1.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 220K 15 \nColorSync 240K 28 \nCoreAnimation 104K 15 \nCoreGraphics 12K 2 \nCoreServices 812K 3 \nCoreUI image data 3232K 22 \nFoundation 16K 1 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 1.1G 653 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 120K 30 \nStack 181.2M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 232.8M 104 \n__CTF 756 1 \n__DATA 47.1M 745 \n__DATA_CONST 40.6M 377 \n__DATA_DIRTY 1817K 223 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__LINKEDIT 213.6M 149 \n__OBJC_RO 65.5M 1 \n__OBJC_RW 1989K 2 \n__TEXT 914.1M 745 \ndyld private memory 288K 3 \nmapped file 117.4M 53 \nshared memory 3012K 33 \n=========== ======= ======= \nTOTAL 2.9G 3263 \nTOTAL, minus reserved VM space 2.9G 3263 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "62699e1ec1ff2978b47f6c3b",
"factorPackIds" : {
"SIRI_FIND_MY_CONFIGURATION_FILES" : "631f72d1de559130376df1fb"
},
"deploymentId" : 240000023
},
{
"rolloutId" : "60f8ddccefea4203d95cbeef",
"factorPackIds" : {
},
"deploymentId" : 240000025
}
],
"experiments" : [
{
"treatmentId" : "6dd670af-0633-45e4-ae5f-122ae4df02be",
"experimentId" : "64406ba83deb637ac8a04419",
"deploymentId" : 900000017
}
]
}
}
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/152 mutation .cxs"
Log from Tue Oct 3 09:30:24 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/draft report full spike .cxs"
Log from Tue Oct 3 09:10:46 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/everything together w the 210 mt .cxs"
> format session
Log from Mon Oct 2 21:58:42 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/everything together .cxs"
Log from Mon Oct 2 16:41:54 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/THIS IS THE FIRST GOOD ONE .cxs" format
> session
Log from Mon Oct 2 16:01:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/session 4 .cxs"
Log from Mon Oct 2 15:41:00 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/session 3.cxs"
Log from Mon Oct 2 15:22:51 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/aimeepickford/Desktop/session 2.cxs"
Log from Mon Oct 2 15:10:40 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/aimeepickford/Downloads/7wpa.pdb format pdb
7wpa.pdb title:
Sars-cov-2 ο variant spike trimer complexed with ACE2 [more info...]
Chain information for 7wpa.pdb #1
---
Chain | Description | UniProt
A B C | spike glycoprotein | SPIKE_SARS2 1-1205
D | angiotensin-converting enzyme 2 | ACE2_HUMAN 1-805
Non-standard residues in 7wpa.pdb #1
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)
ZN — zinc ion
> set bgColor white
> show surfaces
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> hide surfaces
> interfaces ~solvent
4 buried areas: B C 5847, A B 5699, A C 4985, A D 881
> show surfaces
> hide surfaces
[Repeated 1 time(s)]
> show surfaces
> hide surfaces
> color bychain
> show surfaces
> select /D:593@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select down
1 atom, 1 residue, 2 models selected
> select down
1 atom, 1 residue, 2 models selected
> save "/Users/aimeepickford/Desktop/session 1 .cxs"
> color (#!1 & sel) lime
> undo
> color sel bychain
> color (#!1 & sel) cyan
> undo
> select /A:343@CG
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
297 atoms, 306 bonds, 36 residues, 2 models selected
> select up
3283 atoms, 3374 bonds, 416 residues, 2 models selected
> select up
3311 atoms, 3400 bonds, 420 residues, 2 models selected
> select down
3283 atoms, 3374 bonds, 416 residues, 2 models selected
> select down
297 atoms, 306 bonds, 36 residues, 2 models selected
> select up
3283 atoms, 3374 bonds, 416 residues, 2 models selected
> select up
3311 atoms, 3400 bonds, 420 residues, 2 models selected
> select up
4947 atoms, 5075 bonds, 626 residues, 2 models selected
> select up
5017 atoms, 5145 bonds, 634 residues, 2 models selected
> select up
7467 atoms, 7650 bonds, 951 residues, 2 models selected
> select up
7563 atoms, 7749 bonds, 962 residues, 2 models selected
> select up
7966 atoms, 8160 bonds, 1014 residues, 2 models selected
> select up
7987 atoms, 8182 bonds, 1016 residues, 2 models selected
> select up
8413 atoms, 8624 bonds, 1067 residues, 2 models selected
> select down
7987 atoms, 8182 bonds, 1016 residues, 2 models selected
> select down
7966 atoms, 8160 bonds, 1014 residues, 2 models selected
> select down
7563 atoms, 7749 bonds, 962 residues, 2 models selected
> select down
7467 atoms, 7650 bonds, 951 residues, 2 models selected
> select down
5017 atoms, 5145 bonds, 634 residues, 2 models selected
> select down
4947 atoms, 5075 bonds, 626 residues, 2 models selected
> select down
3311 atoms, 3400 bonds, 420 residues, 2 models selected
> select down
3283 atoms, 3374 bonds, 416 residues, 2 models selected
> select down
297 atoms, 306 bonds, 36 residues, 2 models selected
> select down
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
297 atoms, 306 bonds, 36 residues, 2 models selected
> select up
3283 atoms, 3374 bonds, 416 residues, 2 models selected
> color (#!1 & sel) orange
> color (#!1 & sel) purple
> color (#!1 & sel) orange
> select clear
> select /A:483@CE2
1 atom, 1 residue, 1 model selected
Alignment identifier is 1/A
> select#1/B:152
Unknown command: select#1/B:152
> select#1/B:40-400
Unknown command: select#1/B:40-400
> select #1/B:40-400
2545 atoms, 2614 bonds, 4 pseudobonds, 312 residues, 2 models selected
> select #1/B:152
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> undo
> select #1/A:152
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> select /A:531@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
91 atoms, 91 bonds, 12 residues, 2 models selected
> select up
3283 atoms, 3374 bonds, 416 residues, 2 models selected
> select up
3311 atoms, 3400 bonds, 420 residues, 2 models selected
> select up
4947 atoms, 5075 bonds, 626 residues, 2 models selected
> select up
5017 atoms, 5145 bonds, 634 residues, 2 models selected
> select up
7467 atoms, 7650 bonds, 951 residues, 2 models selected
> select up
7563 atoms, 7749 bonds, 962 residues, 2 models selected
> select up
7966 atoms, 8160 bonds, 1014 residues, 2 models selected
> select up
7987 atoms, 8182 bonds, 1016 residues, 2 models selected
> color (#!1 & sel) orange
> select up
8413 atoms, 8624 bonds, 1067 residues, 2 models selected
> color (#!1 & sel) orange
> select up
30444 atoms, 31229 bonds, 3821 residues, 2 models selected
> color (#!1 & sel) orange
> undo
> select clear
> select #1/A:152
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) lime
> select #1/A:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) lime
> select /A
8413 atoms, 8624 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> hide sel atoms
> hide #1/B-C
> hide #1/B,C
> hide #1/B
> hide sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> hide sel surfaces
> undo
[Repeated 1 time(s)]
> hide #1/B surfaces
> hide sel atoms
> hide #1/C surfaces
> hide
> Sel #1/B
Unknown command: Sel #1/B
> Sel 1/B
Unknown command: Sel 1/B
> select #1/B
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> select #1/A
8413 atoms, 8624 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> show sel surfaces
> select #1/B
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/C
8381 atoms, 8585 bonds, 8 pseudobonds, 1063 residues, 2 models selected
> cartoon hide (#!1 & sel)
> select #1/A:210
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) lime
> select #1/A:257
Nothing selected
> select #1/A:257
Nothing selected
> select #1/A:257
Nothing selected
> select #1/A:339
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) lime
> select #1/A:446
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!1 & sel) lime
> select #1/A:460
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) lime
> select #1/A:460
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
[Repeated 1 time(s)]
> save "/Users/aimeepickford/Desktop/session 2.cxs"
——— End of log from Mon Oct 2 15:10:40 2023 ———
opened ChimeraX session
> select #1/A:460
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel LYS rotLib Dunbrack
/A PRO 460: phi -62.4, psi 149.8 trans
Changed 438 bond radii
> swapaa #!1/A:460 LYS criteria 1 rotLib Dunbrack
Using Dunbrack library
7wpa.pdb #!1/A PRO 460: phi -62.4, psi 149.8 trans
Applying LYS rotamer (chi angles: -67.1 -178.8 -179.7 179.2) to 7wpa.pdb #!1/A
LYS 460
> color (#!1 & sel) lime
> show sel atoms
[Repeated 1 time(s)]
> style sel sphere
Changed 4 atom styles
> hide sel surfaces
> style sel ball
Changed 4 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> show sel atoms
> hide sel surfaces
> select #1/A
8415 atoms, 8625 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> select #1/A:460
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) yellow
> color (#!1 & sel) cyan
> select #1/A
8415 atoms, 8625 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> show sel surfaces
[Repeated 1 time(s)]
> show sel cartoons
> show sel atoms
> select clear
> select #1/A
8415 atoms, 8625 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> show sel cartoons
> hide sel surfaces
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> hide sel atoms
> show sel atoms
> hide sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> undo
> hide sel atoms
> show sel atoms
> show sel cartoons
> hide sel atoms
> show sel atoms
[Repeated 1 time(s)]
> hide sel atoms
> show sel atoms
> select #1/A:446
12 atoms, 12 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> ui tool show Rotamers
[Repeated 1 time(s)]
> swapaa interactive sel SER rotLib Dunbrack
/A TYR 446: phi -90.1, psi 15.1 trans
Changed 9 bond radii
> swapaa #!1/A:446 SER criteria 1 rotLib Dunbrack
Using Dunbrack library
7wpa.pdb #!1/A TYR 446: phi -90.1, psi 15.1 trans
Applying SER rotamer (chi angles: 62.6) to 7wpa.pdb #!1/A SER 446
> select #1/A:339
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> ui tool show Rotamers
[Repeated 1 time(s)]
> swapaa interactive sel HIS rotLib Dunbrack
/A PHE 339: phi -78.6, psi -45.9 trans
Changed 288 bond radii
> swapaa #!1/A:339 HIS criteria 1 rotLib Dunbrack
Using Dunbrack library
7wpa.pdb #!1/A PHE 339: phi -78.6, psi -45.9 trans
Applying HIS rotamer (chi angles: -177.7 69.6) to 7wpa.pdb #!1/A HIS 339
> select #1/A:257
Nothing selected
> select #1/A:210
7 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> ui tool show Rotamers
> swapaa interactive sel VAL rotLib Dunbrack
/A PRO 210: phi -75.0, psi -169.9 trans
Changed 12 bond radii
> swapaa #!1/A:210 VAL criteria 1 rotLib Dunbrack
Using Dunbrack library
7wpa.pdb #!1/A PRO 210: phi -75.0, psi -169.9 trans
Applying VAL rotamer (chi angles: -60.8) to 7wpa.pdb #!1/A VAL 210
> select #1/A:157
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> ui tool show Rotamers
> swapaa interactive sel LEU rotLib Dunbrack
/A SER 157: phi -138.3, psi 149.4 trans
Changed 45 bond radii
> swapaa #!1/A:157 LEU criteria 1 rotLib Dunbrack
Using Dunbrack library
7wpa.pdb #!1/A SER 157: phi -138.3, psi 149.4 trans
Applying LEU rotamer (chi angles: -63.7 170.4) to 7wpa.pdb #!1/A LEU 157
> select #1/A:152
11 atoms, 11 bonds, 1 residue, 1 model selected
> color (#!1 & sel) cyan
> ui tool show Rotamers
> swapaa interactive sel ARG rotLib Dunbrack
/A PHE 152: phi -74.5, psi 77.5 trans
Changed 600 bond radii
> swapaa #!1/A:152 ARG criteria 1 rotLib Dunbrack
Using Dunbrack library
7wpa.pdb #!1/A PHE 152: phi -74.5, psi 77.5 trans
Applying ARG rotamer (chi angles: -65.6 179.9 -179.5 -179.9) to 7wpa.pdb #!1/A
ARG 152
> save "/Users/aimeepickford/Desktop/session 3.cxs"
——— End of log from Mon Oct 2 15:22:51 2023 ———
opened ChimeraX session
> select #1/A:460
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:339
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:152
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A
8410 atoms, 8617 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> color (#!1 & sel) blue
> undo
> color (#!1 & sel) medium blue
> select #1/A:152
11 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:257
Nothing selected
> color red
> undo
> select #1/A:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:257
Nothing selected
> color red
> undo
> select #1/A:339
10 atoms, 10 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> select #1/A:460
9 atoms, 8 bonds, 1 residue, 1 model selected
> color (#!1 & sel) red
> save "/Users/aimeepickford/Desktop/session 4 .cxs"
——— End of log from Mon Oct 2 15:41:00 2023 ———
opened ChimeraX session
> select /D:573@CG1
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 2 models selected
> select up
158 atoms, 160 bonds, 21 residues, 2 models selected
> select up
4899 atoms, 5039 bonds, 598 residues, 2 models selected
> hide sel surfaces
> select clear
> ui mousemode right distance
[Repeated 5 time(s)]
> select /D
4901 atoms, 5039 bonds, 600 residues, 1 model selected
> select sel @< 5
4987 atoms, 5103 bonds, 621 residues, 1 model selected
> color (#!1 & sel) purple
> undo
> select #1/A
8410 atoms, 8617 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> hide sel atoms
> select clear
> select #1/A:446
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:460
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:339
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:257
Nothing selected
> select #1/A:210
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:157
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:152
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> save "/Users/aimeepickford/Desktop/THIS IS THE FIRST GOOD ONE .cxs"
——— End of log from Mon Oct 2 16:01:41 2023 ———
opened ChimeraX session
> transparency #1/B 50
> select #1/b
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> show sel surfaces
> show sel cartoons
> hide sel surfaces
> transparency #1/B 50
> transparency #1/B 90
> transparency#1/B 90
Unknown command: transparency#1/B 90
> transparency #1/B 90
> select clear
> select #1/B
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> color (#!1 & sel) light gray
> transparency #1/B 50
> select #1/C
8381 atoms, 8585 bonds, 8 pseudobonds, 1063 residues, 2 models selected
> show sel surfaces
> show sel cartoons
> hide sel surfaces
> transparency #1/C 90
> select clear
> save "/Users/aimeepickford/Desktop/everything together .cxs"
——— End of log from Mon Oct 2 16:41:54 2023 ———
opened ChimeraX session
> select #1/A:230-270
172 atoms, 175 bonds, 1 pseudobond, 20 residues, 2 models selected
> color (#!1 & sel) red
> save "/Users/aimeepickford/Desktop/everything together w the 210 mt .cxs"
——— End of log from Mon Oct 2 21:58:42 2023 ———
opened ChimeraX session
> select clear
> save "/Users/aimeepickford/Desktop/draft report full spike .cxs"
——— End of log from Tue Oct 3 09:10:46 2023 ———
opened ChimeraX session
> select #1/B
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> color (#!1 & sel) #f2aaffff
> select #1/D
4901 atoms, 5039 bonds, 600 residues, 1 model selected
> select sel @< 5
4987 atoms, 5103 bonds, 621 residues, 1 model selected
> color (#!1 & sel) orange
> select #1/A
8410 atoms, 8617 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> select clear
> save "/Users/aimeepickford/Desktop/receptor interaction w A.cxs"
> select #1/D
4901 atoms, 5039 bonds, 600 residues, 1 model selected
> hide sel cartoons
> select #1/152
Nothing selected
> select #1/A:152
11 atoms, 10 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
0 hydrogen bonds found
> ui tool show "Side View"
> select #1/C
8381 atoms, 8585 bonds, 8 pseudobonds, 1063 residues, 2 models selected
> select #1/B
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> select #1/B
8413 atoms, 8621 bonds, 6 pseudobonds, 1067 residues, 2 models selected
> select clear
> save "/Users/aimeepickford/Desktop/152 mutation .cxs"
——— End of log from Tue Oct 3 09:30:24 2023 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-20.2.50
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,3
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: 1916.80.2.0.0 (iBridge: 20.16.3045.0.0,0)
OS Loader Version: 564.40.4~66
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 17 days, 16 hours, 10 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: 0.7.13
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
build: 0.10.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
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: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
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: 1.6.1
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: 1.1.1
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-Label: 1.1.7
ChimeraX-ListInfo: 1.1.1
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: 2.0.12
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: 1.3.7
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: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
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: 1.1
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: 2.8.3
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
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
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: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
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: 1.0.7
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: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.2.22
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
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: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
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: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
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 13.2.1, Intel Iris Plus Graphics 645 |
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Apple Intel graphics driver crash.