![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 11 months ago
Last modified 11 months ago
#16413 feedback defect
Crash checking for changes during "lighting soft"
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.1.1-x86_64-i386-64bit
ChimeraX Version: 1.9rc202412032254 (2024-12-03 22:54:16 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
The structure is with grey noise when I selected soft light
Fatal Python error: Bus error
Current thread 0x00007ff8457f9b40 (most recent call first):
File "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2233 in changed
File "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 31 in check_for_changes
File "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.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 "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 335 in event_loop
File "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/private/var/folders/6f/30_dn2lj0rl64x6_7nxtspkw0000gn/T/AppTranslocation/EA825F87-E85B-4984-BDA7-4EFED27249B6/d/ChimeraX_Daily.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
{"app_name":"ChimeraX","timestamp":"2024-12-04 11:43:29.00 -0500","app_version":"","slice_uuid":"d03aaccc-552e-37c3-815c-2eab08da2961","build_version":"","platform":1,"share_with_app_devs":0,"is_first_party":1,"bug_type":"309","os_version":"macOS 15.1.1 (24B91)","roots_installed":0,"incident_id":"2808ADD4-B992-4B91-BEC8-24A6D0846D2D","name":"ChimeraX"}
{
"uptime" : 47000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 34011,
"osVersion" : {
"train" : "macOS 15.1.1",
"build" : "24B91",
"releaseType" : "User"
},
"captureTime" : "2024-12-04 11:43:28.7218 -0500",
"codeSigningMonitor" : 0,
"incident" : "2808ADD4-B992-4B91-BEC8-24A6D0846D2D",
"pid" : 24559,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-12-04 11:41:08.5646 -0500",
"procStartAbsTime" : 46989982009839,
"procExitAbsTime" : 47130149264027,
"procName" : "ChimeraX",
"procPath" : "\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C4AF4742-205C-64C7-D807-E542FF6C19C4",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bootSessionUUID" : "39B56EF1-7126-4190-B594-02117D279206",
"wakeTime" : 7207,
"bridgeVersion" : {"build":"22P1072","train":"9.1"},
"sleepWakeUUID" : "1F52F741-C248-48FD-B648-0234572F1F21",
"sip" : "enabled",
"vmRegionInfo" : "0x1024c55d0 is in 0x102290000-0x102668000; bytes after start: 2315728 bytes before end: 1714735\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC guard page 10228f000-102290000 [ 4K] ---\/rwx SM=SHM \n---> mapped file 102290000-102668000 [ 3936K] r-x\/rwx SM=COW Object_id=bc0b51f3\n mapped file 102668000-1027b8000 [ 1344K] rw-\/rwx SM=COW Object_id=3261a9b2",
"exception" : {"codes":"0x000000000000000a, 0x00000001024c55d0","rawCodes":[10,4333524432],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_MEMORY_ERROR at 0x00000001024c55d0"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"exc handler","byPid":24559},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0x1024c55d0 is in 0x102290000-0x102668000; bytes after start: 2315728 bytes before end: 1714735\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n MALLOC guard page 10228f000-102290000 [ 4K] ---\/rwx SM=SHM \n---> mapped file 102290000-102668000 [ 3936K] r-x\/rwx SM=COW Object_id=bc0b51f3\n mapped file 102668000-1027b8000 [ 1344K] rw-\/rwx SM=COW Object_id=3261a9b2",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
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"vmSummary" : "ReadOnly portion of Libraries: Total=182.6M resident=0K(0%) swapped_out_or_unallocated=182.6M(100%)\nWritable regions: Total=1.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 204K 23 \nColorSync 240K 30 \nCoreAnimation 460K 51 \nCoreGraphics 12K 2 \nCoreUI image data 2868K 21 \nFoundation 16K 1 \nIOKit 7940K 1 \nKernel Alloc Once 8K 1 \nMALLOC 839.6M 402 \nMALLOC guard page 48K 12 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 108K 27 \nStack 186.7M 28 \nStack Guard 56.0M 1 \nVM_ALLOCATE 237.6M 183 \nVM_ALLOCATE (reserved) 56K 2 reserved VM address space (unallocated)\n__DATA 11K 1 \n__DATA_CONST 23K 1 \n__DATA_DIRTY 7K 1 \n__LINKEDIT 182.0M 1 \n__TEXT 564K 1 \n__TPRO_CONST 272K 1 \ndyld private memory 292K 3 \nmapped file 642.7M 558 \nowned unmapped memory 39.9M 1 \nshared memory 3768K 35 \n=========== ======= ======= \nTOTAL 2.2G 1398 \nTOTAL, minus reserved VM space 2.2G 1398 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain"
}
},
"logWritingSignature" : "fa4120f41de226a0ba78437d137a5f20d9cbf8f9",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "64c17a9925d75a7281053d4c",
"factorPackIds" : {
"SIRI_AUDIO_DISABLE_MEDIA_ENTITY_SYNC" : "64d29746ad29a465b3bbeace"
},
"deploymentId" : 240000002
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
},
"deploymentId" : 240000451
}
],
"experiments" : [
]
}
}
===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202412030600 (2024-12-03)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Paper Figure
> 5/Mutated_Epitope_Schematic.cxs"
Log from Wed Dec 4 00:07:14 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Paper Figure
> 5/Mutated_Epitope_Schematic.cxs"
Log from Tue Dec 3 23:41:07 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Paper Figure
> 5/0_mutation_figures.cxs"
Log from Sun Oct 20 14:47:44 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open /Users/frankfeng/Desktop/0_mutation_figures.cxs
Log from Sat Oct 19 22:12:48 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Paper Figure 5/Figure5.A.KP311.cxs"
Log from Wed Oct 2 15:26:17 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Paper Figure 5/Figure5.A.cxs"
Log from Sat Sep 28 15:14:38 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Figure 5/RBD_Mutation.cxs"
Log from Mon Sep 23 21:10:46 2024UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
> open "/Users/frankfeng/Desktop/Figures/Figure 5/mutation.cxs"
Log from Tue Sep 10 02:08:34 2024 Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/frankfeng/Desktop/rbd_curve.pdb
Chain information for rbd_curve.pdb #1
---
Chain | Description
E | No description available
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> set bgColor white
> show atoms
> style sphere
Changed 1545 atom styles
> select all
1545 atoms, 1583 bonds, 203 residues, 1 model selected
> color sel gray
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'o' for virtual key 31 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'O' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00f8' for virtual key 31 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00d8' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xf' for virtual key 31 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select
> #1/E:339,341,346,366,370,377,384,392,395,413,417,418,419,429,446,452,477,478,481,483,484,486,489,492,493,498,501,505,508,513,521,524
261 atoms, 243 bonds, 32 residues, 1 model selected
> lighting soft
> color sel #d15c6bff
> color sel #ba6d74ff
[Repeated 1 time(s)]
> color sel #ac656bff
> view
> color sel #ac777cff
[Repeated 1 time(s)]
> color sel #ac8185ff
[Repeated 1 time(s)]
> color sel #ac6e73ff
> color sel #ac6e72ff
> color sel #ac757aff
[Repeated 1 time(s)]
> color sel #b77d81ff
[Repeated 3 time(s)]
> color sel #b67c81ff
[Repeated 1 time(s)]
> color sel #b57c80ff
[Repeated 1 time(s)]
> color sel #b47b80ff
[Repeated 1 time(s)]
> view
> save figure5.A1.png supersample 4
> select #2
Nothing selected
> set silhouettes true
> save figure5.A1.png supersample 4
> turn x 180
> save figure5.A2.png supersample 4
> open /Users/frankfeng/Desktop/rbd_curve.pdb
Chain information for rbd_curve.pdb #2
---
Chain | Description
E | No description available
6 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #1 models
> select
> #2/E:339,341,346,366,370,377,384,392,395,413,417,418,419,429,446,452,477,478,481,483,484,486,489,492,493,498,501,505,508,513,521,524
261 atoms, 243 bonds, 32 residues, 1 model selected
> select #2
1545 atoms, 1583 bonds, 203 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 1545 atom styles
> color sel gray
> select
> #2/E:339,341,346,366,370,377,384,392,395,413,417,418,419,429,446,452,477,478,481,483,484,486,489,492,493,498,501,505,508,513,521,524
261 atoms, 243 bonds, 32 residues, 1 model selected
> color sel #b47b80ff
[Repeated 1 time(s)]
> move x 10 models #2
[Repeated 1 time(s)]
> show #1 models
> move x 10 models #2
[Repeated 2 time(s)]
> turn x 180 models #2
[Repeated 1 time(s)]
> turn y 180 models #2
[Repeated 8 time(s)]
> turn z 90 models #2
[Repeated 5 time(s)]
> turn x 180 models #2
> hide #2 models
> view
> save figure5.A2.png supersample 4
> select #1/E:339
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/E:346
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #1/E:395
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/E:418
8 atoms, 7 bonds, 1 residue, 1 model selected
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #1/E:419
5 atoms, 4 bonds, 1 residue, 1 model selected
> select #1/E:446
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #1/E:481
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #1/E:483
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #1/E:488
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #1/E:492
8 atoms, 7 bonds, 1 residue, 1 model selected
> 508
Unknown command: 508
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #1/E:508
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #1/E:513
8 atoms, 7 bonds, 1 residue, 1 model selected
> save /Users/frankfeng/Desktop/mutation.cxs
——— End of log from Tue Sep 10 02:08:34 2024 ———
opened ChimeraX session
> select #1
1545 atoms, 1583 bonds, 203 residues, 1 model selected
> select subtract #1:339,346,417,452,477,478,481,483,484,486,493,498,501,505
1427 atoms, 1451 bonds, 189 residues, 1 model selected
> color sel gray
> select #1:339,346,417,452,477,478,481,483,484,486,493,498,501,505
118 atoms, 108 bonds, 14 residues, 1 model selected
> select #2
1545 atoms, 1583 bonds, 203 residues, 1 model selected
> save /Users/frankfeng/Desktop/RBD_mutation.cxs
> view
[Repeated 3 time(s)]
> save figure5.A1.png supersample 4
> turn 180
Expected an axis vector or a keyword
> view
[Repeated 1 time(s)]
> save figure5.A1.png supersample 4
> turn x 180
> save figure5.A2.png supersample 4
> show ligand
> close #1
> close
> open 6m0j
6m0j title:
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]
Chain information for 6m0j #1
---
Chain | Description | UniProt
A | Angiotensin-converting enzyme 2 | ACE2_HUMAN 19-615
E | Spike protein S1 | SPIKE_SARS2 319-541
Non-standard residues in 6m0j #1
---
CL — chloride ion
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ZN — zinc ion
13 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> select #1/A
4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected
> delete #1/A
> select #1
1559 atoms, 1598 bonds, 204 residues, 1 model selected
> hide ligand
> show ligand
> color sel gray
> hide ligand
> show sel atoms
> style sel sphere
Changed 1559 atom styles
> show ligand
[Repeated 1 time(s)]
> undo
[Repeated 3 time(s)]
> show ligand
> hide ligand
> show sel atoms
> style sel sphere
Changed 1559 atom styles
> show ligand
> hide ligand
> show ligand
> select ligand
14 atoms, 14 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide sel atoms
> show sel cartoons
> show sel atoms
> style sel stick
Changed 14 atom styles
> select #1/E:339,346,417,452,477,478,481,483,484,486,493,498,501,505
118 atoms, 108 bonds, 14 residues, 1 model selected
> color sel #ffa093ff
> color sel #ffa092ff
> color sel #ff7f6eff
[Repeated 1 time(s)]
> color sel #ff7d4bff
> color sel #ff7c4aff
> color sel #ff5a7aff
[Repeated 1 time(s)]
> color sel #ff8598ff
[Repeated 1 time(s)]
> color sel #ff816fff
[Repeated 1 time(s)]
> color sel #ff9097ff
[Repeated 1 time(s)]
> color sel #c87176ff
[Repeated 1 time(s)]
> color sel #ab6165ff
> color sel #ab6065ff
> color sel #bf6d72ff
[Repeated 2 time(s)]
> color sel #bf5b5dff
> color sel #bf5a5dff
> color sel #bf596dff
[Repeated 1 time(s)]
> color sel #bf635cff
[Repeated 1 time(s)]
> color sel #bf6c5bff
[Repeated 1 time(s)]
> color sel #bf4b4cff
[Repeated 1 time(s)]
> color sel #ae4445ff
[Repeated 1 time(s)]
> color sel #ae5554ff
[Repeated 1 time(s)]
> color sel #ae6866ff
> save /Users/frankfeng/Desktop/RBD_Mutation.cxs
——— End of log from Mon Sep 23 21:10:46 2024 ———
opened ChimeraX session
> select all
1559 atoms, 1598 bonds, 204 residues, 1 model selected
> color sel white
> select
> #1/E:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,460,477,478,481,483,484,486,493,496,498,501,505
218 atoms, 196 bonds, 28 residues, 1 model selected
> color sel #e3716eff
> color sel #caadd8ff
> color sel #af8fd0ff
> select all
1559 atoms, 1598 bonds, 204 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> color sel white
> select
> #1/E:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,460,477,478,481,483,484,486,493,496,498,501,505
218 atoms, 196 bonds, 28 residues, 1 model selected
> style sel sphere
Changed 218 atom styles
> show sel atoms
> select #1/E:601
14 atoms, 14 bonds, 1 residue, 1 model selected
> style sel stick
Changed 14 atom styles
> show sel atoms
> hide sel cartoons
> hide sel atoms
> select
> #1/E:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,460,477,478,481,483,484,486,493,496,498,501,505
218 atoms, 196 bonds, 28 residues, 1 model selected
> color sel #f6ecf6ff
> color sel #efc0d2ff
> color sel #d93f49ff
> color sel #e28187ff
> color sel #ebbfc2ff
> undo
> color sel #e19d92ff
> cartoon style thickness 2
> lighting soft
> color sel #b31c3dff
> color sel #f0776dff
> color sel #9f1f31ff
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 's' for virtual key 1 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'S' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00df' for virtual key 1 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00cd' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x13' for virtual key 1 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> select #2
Nothing selected
> save "/Users/frankfeng/Desktop/Figures/Paper Figure 5/Figure5.A.cxs"
——— End of log from Sat Sep 28 15:14:38 2024 ———
opened ChimeraX session
> select #1/E:496
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel white
> select #1/E:456
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel #9f1f31ff
> select #2
Nothing selected
> view
> save Figure5.A1.png width 3440 height 2560 transparentBackground true
> supersample 4
> graphics silhouettes width 3.5
> save Figure5.A1.png width 3440 height 2560 transparentBackground true
> supersample 4
> save Figure5.A2.png width 3440 height 2560 transparentBackground true
> supersample 4
> save "/Users/frankfeng/Desktop/Figures/Paper Figure 5/Figure5.A.KP311.cxs"
——— End of log from Wed Oct 2 15:26:17 2024 ———
opened ChimeraX session
> open S304
'S304' has no suffix
> open 8HWT
Summary of feedback from opening 8HWT fetched from pdb
---
note | Fetching compressed mmCIF 8hwt from http://files.rcsb.org/download/8hwt.cif
8hwt title:
SARS-CoV-2 ο BA.2 RBD complexed with BD-604 and S304 Fab [more info...]
Chain information for 8hwt #2
---
Chain | Description | UniProt
A | Spike protein S2' | SPIKE_SARS2 319-541
D | S304 heavy chain |
E | S304 light chain |
H | BD-604 heavy chain |
L | BD-604 light chain |
9 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete #2/H/L
> mmaker #2/A to #1/E
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 6m0j, chain E (#1) with 8hwt, chain A (#2), sequence alignment
score = 1017.8
RMSD between 183 pruned atom pairs is 0.731 angstroms; (across all 188 pairs:
0.896)
> select
> #2/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
239 atoms, 223 bonds, 28 residues, 1 model selected
> select #2/A
1515 atoms, 1564 bonds, 1 pseudobond, 189 residues, 2 models selected
> color (#!2 & sel) gray
> close #1
> select all
4819 atoms, 4951 bonds, 1 pseudobond, 626 residues, 2 models selected
> lighting soft
> graphics silhouettes false
> select
> #2/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
239 atoms, 223 bonds, 28 residues, 1 model selected
> color sel #9f1f31ff
> select #2/D/E
3304 atoms, 3387 bonds, 437 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> graphics silhouettes width 3.5
[Repeated 1 time(s)]
> set silhouettes true
> graphics silhouettes width 3.5
> cartoon style thickness 2
> color sel bychain
> select #2/H
Nothing selected
> select #2/D
1662 atoms, 1706 bonds, 222 residues, 1 model selected
> ui tool show "Color Actions"
> color sel light cyan
> color sel lavender
> select #2/E
1642 atoms, 1680 bonds, 215 residues, 1 model selected
> color sel gainsboro
> color sel wheat
> color sel beige
> select 3
Expected an objects specifier or a keyword
> select #3
Nothing selected
> interfaces ~solvent
3 buried areas: D E 1875, D A 441, E A 376
> ui tool show "Color Actions"
> color sel sky blue
> color sel light sky blue
[Repeated 1 time(s)]
> color sel light blue
> color sel pale turquoise
> color sel light steel blue
[Repeated 2 time(s)]
> select #2/D/E
3304 atoms, 3387 bonds, 437 residues, 1 model selected
> transparency 80 cartoons
> transparency 65 cartoons
> transparency 50 cartoons
> select #3
Nothing selected
> graphics silhouettes width 2
> graphics silhouettes width 3.5
> graphics silhouettes width 2
> transparency 30 cartoons
> transparency 20 cartoons
> transparency 10 cartoons
> transparency 0 cartoons
> transparency 5 cartoons
> transparency 2 cartoons
> transparency 1 cartoons
> transparency 10 cartoons
> select #2/D
1662 atoms, 1706 bonds, 222 residues, 1 model selected
> ui tool show "Color Actions"
> color sel dark violet
> color sel blue violet
> color sel light coral
[Repeated 1 time(s)]
> select #2/E
1642 atoms, 1680 bonds, 215 residues, 1 model selected
> color sel burly wood
> select #3/D
Nothing selected
> select #3/D/E
Nothing selected
> select #2/D/E
3304 atoms, 3387 bonds, 437 residues, 1 model selected
> transparency 10 cartoons
> transparency 50 cartoons
> transparency 80 cartoons
> select #2/A
1515 atoms, 1564 bonds, 1 pseudobond, 189 residues, 2 models selected
> show sel surfaces
[Repeated 1 time(s)]
> show sel atoms
> hide sel atoms
> show sel atoms
> show sel surfaces
[Repeated 2 time(s)]
> select #2/A surface
Expected a keyword
> select #2/A
1515 atoms, 1564 bonds, 1 pseudobond, 189 residues, 2 models selected
> show sel cartoons
> hide sel atoms
> hide sel cartoons
> hide sel surfaces
> show sel surfaces
> color (#!2 & sel) gray
> select
> #2/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
239 atoms, 223 bonds, 28 residues, 1 model selected
> ui tool show "Color Actions"
> color (#!2 & sel) #a35c45ff
[Repeated 1 time(s)]
> color (#!2 & sel) #a34049ff
[Repeated 2 time(s)]
> color (#!2 & sel) #9f1f31ff
> select #3
Nothing selected
> interfaces ~solvent
3 buried areas: D E 1875, D A 441, E A 376
> interfaces ~solvent
3 buried areas: D E 1875, D A 441, E A 376
> interfaces ~solvent
3 buried areas: D E 1875, D A 441, E A 376
> ui tool show "Color Actions"
> color sel light steel blue
> color sel light sky blue
> color sel powder blue
> color sel silver
> color sel light gray
> color sel thistle
> color sel slate blue
> color sel gray
> color sel dark sea green
> color sel dark gray
> color sel lavender blush
> color sel blanched almond
> color sel bisque
> color sel navajo white
> color sel light blue
> color sel light steel blue
[Repeated 1 time(s)]
> select #2/D/E
3304 atoms, 3387 bonds, 437 residues, 1 model selected
> transparency 90 cartoons
> transparency 85 cartoons
> save /Users/frankfeng/Desktop/0_mutation_figures.cxs
——— End of log from Sat Oct 19 22:12:48 2024 ———
opened ChimeraX session
> open 8CY9
8cy9 title:
SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 1-23
[more info...]
Chain information for 8cy9 #1
---
Chain | Description | UniProt
A B C | Spike glycoprotein | SPIKE_SARS2 1-1273
D E F | pan-sarbecovirus nanobody 1-23 |
> mmaker #1/A to #2/A
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 8hwt, chain A (#2) with 8cy9, chain A (#1), sequence alignment
score = 965.6
RMSD between 157 pruned atom pairs is 0.989 angstroms; (across all 189 pairs:
1.671)
> delete #1/B/C/E/F
> delete #1/A & ~#1/A:333-527
> select #2
4819 atoms, 4951 bonds, 1 pseudobond, 626 residues, 2 models selected
> move y -10 true
Expected an integer >= 1 or a keyword
> move y -10 #2
Expected an integer >= 1 or a keyword
> move y -10 #2
Expected an integer >= 1 or a keyword
> move y -10 models #2
[Repeated 5 time(s)]
> move y 10 models #2
[Repeated 12 time(s)]
> move x -10 models #2
[Repeated 1 time(s)]
> select #1/A
1543 atoms, 1591 bonds, 195 residues, 1 model selected
> color sel gray
> show sel surfaces
> select
> #1/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
225 atoms, 205 bonds, 28 residues, 1 model selected
> color (#!1 & sel) #9f1f31ff
> select #1/D
906 atoms, 924 bonds, 121 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> cartoon style thickness 2
> transparency 85 cartoons
> ui tool show "Color Actions"
> color sel teal
> color sel light pink
> color sel blanched almond
> color sel deep pink
> color sel magenta
> color sel rebecca purple
> select #2
4819 atoms, 4951 bonds, 1 pseudobond, 626 residues, 2 models selected
> select #3
Nothing selected
> hide #!1 models
> show #!1 models
> hide #!2 models
> interfaces #!1 & ~solvent
1 buried areas: A D 866
> ui tool show "Color Actions"
> color sel light steel blue
> show #!2 models
> save /Users/frankfeng/Desktop/0_mutation_figures.cxs
> open 7U2D
7u2d title:
Crystal structure of SARS-CoV-2 receptor binding domain in complex with
neutralizing antibody ADG20 [more info...]
Chain information for 7u2d #3
---
Chain | Description | UniProt
A | Spike protein S1 | SPIKE_SARS2 333-530
H | ADG20 heavy chain |
L | ADG20 light chain |
Non-standard residues in 7u2d #3
---
CIT — citric acid
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
SO4 — sulfate ion
11 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> mmaker #3/A to #2/E
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 8hwt, chain E (#2) with 7u2d, chain A (#3), sequence alignment
score = 27.6
RMSD between 8 pruned atom pairs is 1.490 angstroms; (across all 88 pairs:
18.735)
> mmaker #3/A to #2/A
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 8hwt, chain A (#2) with 7u2d, chain A (#3), sequence alignment
score = 921.7
RMSD between 181 pruned atom pairs is 0.754 angstroms; (across all 188 pairs:
0.964)
> move x 10 models #3
[Repeated 10 time(s)]
> select #3/A
1562 atoms, 1603 bonds, 203 residues, 1 model selected
> show sel surfaces
> color (#!3 & sel) gray
> delete ligand
> select #3/A
1543 atoms, 1584 bonds, 201 residues, 1 model selected
> select #3/A:403, 405, 408, 498, 501, 505
59 atoms, 54 bonds, 6 residues, 1 model selected
> color (#!3 & sel) #9f1f32ff
> color (#!3 & sel) #9f1f31ff
> select #3/H/L
3267 atoms, 3326 bonds, 1 pseudobond, 461 residues, 2 models selected
> cartoon style thickness 2
> transparency 85 cartoons
> select #3/H
1664 atoms, 1693 bonds, 1 pseudobond, 235 residues, 2 models selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel beige
> color sel light green
> color sel slate blue
> select #4
Nothing selected
> select #3
4810 atoms, 4910 bonds, 1 pseudobond, 662 residues, 2 models selected
> delete ligand
> delete H
> style sel stick
Changed 4810 atom styles
> style sel stick
Changed 4810 atom styles
> style sel sphere
Changed 4810 atom styles
> hide sel cartoons
> show sel cartoons
> hide sel atoms
> open 8Q93
8q93 title:
Crystal structure of the SARS-COV-2 RBD with neutralizing-VHHs Re30H02 and
Re21D01 [more info...]
Chain information for 8q93 #4
---
Chain | Description | UniProt
A | Spike protein S1 | SPIKE_SARS2 334-526
B | Nanobody Re21D01 |
C | Nanobody Re30H02 |
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete #4/B
> delete #4/A
> close #4
> open 8Q93
8q93 title:
Crystal structure of the SARS-COV-2 RBD with neutralizing-VHHs Re30H02 and
Re21D01 [more info...]
Chain information for 8q93 #4
---
Chain | Description | UniProt
A | Spike protein S1 | SPIKE_SARS2 334-526
B | Nanobody Re21D01 |
C | Nanobody Re30H02 |
8 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> delete #4/B
> select #4/A
1532 atoms, 1579 bonds, 194 residues, 1 model selected
> select #4/C
982 atoms, 1009 bonds, 130 residues, 1 model selected
> mmaker #4/C to #1/E
No 'to' model specified
> mmaker #4/C to #1/A
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 8cy9, chain A (#1) with 8q93, chain C (#4), sequence alignment
score = 5.5
RMSD between 6 pruned atom pairs is 0.926 angstroms; (across all 99 pairs:
19.068)
> mmaker #4/A to #1/A
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 8cy9, chain A (#1) with 8q93, chain A (#4), sequence alignment
score = 926
RMSD between 157 pruned atom pairs is 1.059 angstroms; (across all 194 pairs:
3.157)
> move x 10 models #4
[Repeated 10 time(s)]
> move y -10 models #4
[Repeated 1 time(s)]
> move y -10 models #2
> move y -10 models #1
[Repeated 1 time(s)]
> select #4/C
982 atoms, 1009 bonds, 130 residues, 1 model selected
> select #4/A
1532 atoms, 1579 bonds, 194 residues, 1 model selected
> color sel dark gray
> color sel gray
> show sel surfaces
> delete #4/A & ~#4/A:333-527
> select #4/C
982 atoms, 1009 bonds, 130 residues, 1 model selected
> transparency 85 cartoons
> cartoon style thickness 2
> ui tool show "Color Actions"
> color sel medium purple
> color sel orchid
> select #4/A
1532 atoms, 1579 bonds, 194 residues, 1 model selected
> select #4/A:403, 417, 446, 452, 455, 456, 484, 486, 493, 498, 501, 505
109 atoms, 101 bonds, 12 residues, 1 model selected
> color (#!4 & sel) #9f8631ff
[Repeated 1 time(s)]
> color (#!4 & sel) #9f1f31ff
> lighting simple
> lighting soft
> save /Users/frankfeng/Desktop/0_mutation_figures.cxs
——— End of log from Sun Oct 20 14:47:44 2024 ———
opened ChimeraX session
> select up
598 atoms, 609 bonds, 75 residues, 1 model selected
> select #2/A
1515 atoms, 1564 bonds, 1 pseudobond, 189 residues, 2 models selected
> color (#!2 & sel) white
> select #4/A:333-527
1532 atoms, 1579 bonds, 194 residues, 1 model selected
> select
> #2/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
239 atoms, 223 bonds, 28 residues, 1 model selected
> color (#!2 & sel) byhetero
> color (#!2 & sel) #660f1aff
> select #3/A
1543 atoms, 1584 bonds, 201 residues, 1 model selected
> color (#!3 & sel) white
> select #1/A
1543 atoms, 1591 bonds, 195 residues, 1 model selected
> color (#!1 & sel) white
> set silhouettes true
> hide #!4 models
> show #!4 models
> open 7JVB
7jvb title:
Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with
nanobody Nb20 [more info...]
Chain information for 7jvb #5
---
Chain | Description | UniProt
A B | Spike protein S1 | SPIKE_SARS2 319-541
C D | Nanobody Nb20 |
Non-standard residues in 7jvb #5
---
CAC — cacodylate ion (dimethylarsinate)
7jvb mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> hide #5 models
> show #5 models
> close #5
> open 7JVB
7jvb title:
Crystal structure of the SARS-CoV-2 spike receptor-binding domain (RBD) with
nanobody Nb20 [more info...]
Chain information for 7jvb #5
---
Chain | Description | UniProt
A B | Spike protein S1 | SPIKE_SARS2 319-541
C D | Nanobody Nb20 |
Non-standard residues in 7jvb #5
---
CAC — cacodylate ion (dimethylarsinate)
7jvb mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
> mmaker #5/A to #4/A
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 8q93, chain A (#4) with 7jvb, chain A (#5), sequence alignment
score = 917.6
RMSD between 167 pruned atom pairs is 0.840 angstroms; (across all 193 pairs:
2.802)
> hide #!4 models
> delete #5/B
> delete #5/D
> hide ligand
> select #5/A
1517 atoms, 1562 bonds, 195 residues, 1 model selected
> show sel surfaces
> color (#!5 & sel) light gray
> color (#!5 & sel) white
> select #5/C
857 atoms, 871 bonds, 118 residues, 1 model selected
> transparency 80 cartoons
> cartoon width 3
Expected an atoms specifier or a keyword
> graphics silhouettes width 3.5
> show sel cartoons
[Repeated 1 time(s)]
> hide sel cartoons
> show sel cartoons
> graphics silhouettes width 1
> graphics silhouettes width 2
> cartoon style thickness 2
> select
> #1/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
225 atoms, 205 bonds, 28 residues, 1 model selected
> color (#!1 & sel) #660f1aff
> select #1
2449 atoms, 2515 bonds, 316 residues, 1 model selected
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui windowfill toggle
[Repeated 1 time(s)]
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
Alignment identifier is 1/A
Alignment identifier is 1/D
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> ui tool show Contacts
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
Destroying pre-existing alignment with identifier 1/A
Alignment identifier is 1/A
Destroying pre-existing alignment with identifier 1/D
Alignment identifier is 1/D
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> interfaces select #1/A,D
Missing required "contacting" argument
> save "/Users/frankfeng/Desktop/Figures/Figure
> 5/Mutated_Epitope_Schematic.cxs"
——— End of log from Tue Dec 3 23:41:07 2024 ———
opened ChimeraX session
> select #10
Nothing selected
> interfaces #!1-3,5 & ~solvent
7 buried areas: #2/D #2/E 1875, #3/H #3/L 1833, #1/A #1/D 866, #5/A #5/C 758,
#3/H #3/A 489, #2/D #2/A 441, #2/E #2/A 376
> interfaces select #2/A,E
Missing required "contacting" argument
> select #2A:369,378,379,380,381,382,384,385,386,390,412,427,429
Expected an objects specifier or a keyword
> select #2/A:369,378,379,380,381,382,384,385,386,390,412,427,429
107 atoms, 105 bonds, 13 residues, 1 model selected
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!5 models
> hide #!1 models
> show #!3 models
> hide #!3 models
> show #!3 models
> show #!1 models
> show #!4 models
> hide #!4 models
> show #!5 models
> hide #!5 models
> hide #!3 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> hide #!1 models
> save Figure5.C1.png width 3440 height 2560 transparentBackground true
> supersample 4
> show #!1 models
> hide #!2 models
> select up
281 atoms, 287 bonds, 35 residues, 2 models selected
> select #1/A:369,378,379,380,381,382,384,385,386,390,412,427,429
107 atoms, 105 bonds, 13 residues, 1 model selected
> select
> #1/A:380,381,386,394,396,412,413,427,428,429,430,463,464,514,516,517,518,519
149 atoms, 147 bonds, 18 residues, 1 model selected
> save Figure5.C2.png width 3440 height 2560 transparentBackground true
> supersample 4
> save Figure5.C2.png width 3440 height 2560 true supersample 4
Expected a keyword
> save Figure5.C2.png width 3440 height 2560 supersample 4
> show #!2 models
> hide #!1 models
> select #2/A:369,378,379,380,381,382,384,385,386,390,412,427,429
107 atoms, 105 bonds, 13 residues, 1 model selected
> save Figure5.C1.png width 3440 height 2560 supersample 4
> hide #!2 models
> show #!3 models
> select
> #3/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
225 atoms, 205 bonds, 28 residues, 1 model selected
> color (#!3 & sel) #660f1aff
> select #3/A:403,405,408,498,500,501,502,503,504,505,506
90 atoms, 86 bonds, 11 residues, 1 model selected
> save Figure5.C3.png width 3440 height 2560 supersample 4
> hide #!3 models
> show #!5 models
> select
> #5/A:339,356,371,373,375,376,403,405,408,417,440,445,446,450,452,455,456,460,477,478,481,483,484,486,493,498,501,505
225 atoms, 205 bonds, 28 residues, 1 model selected
> color (#!5 & sel) #660f1aff
> show #!3 models
> show #!1 models
> show #!2 models
> select #5/C
857 atoms, 871 bonds, 118 residues, 1 model selected
> ui tool show "Color Actions"
> color sel wheat
> save "/Users/frankfeng/Desktop/Figures/Paper Figure
> 5/Mutated_Epitope_Schematic.cxs"
——— End of log from Wed Dec 4 00:07:14 2024 ———
opened ChimeraX session
> lighting soft
> lighting simple
> lighting soft
> lighting full
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9rc202412032254 (2024-12-03)
© 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 OpenGL Engine
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: MacBookPro16,2
Processor Name: Quad-Core Intel Core i5
Processor Speed: 2 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2069.40.2.0.0 (iBridge: 22.16.11072.0.0,0)
OS Loader Version: 582~2132
Software:
System Software Overview:
System Version: macOS 15.1.1 (24B91)
Kernel Version: Darwin 24.1.0
Time since boot: 1 day, 14 hours, 43 minutes
Graphics/Displays:
Intel Iris Plus Graphics:
Chipset Model: Intel Iris Plus Graphics
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x8a53
Revision ID: 0x0007
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
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: 2.7.1
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: 1.58.7
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: 2.4.7
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: 1.9rc202412032254
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: 1.1.12
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: 4.55.1
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h5py: 3.12.1
html2text: 2024.2.26
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
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 (3)
comment:1 by , 11 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash checking for changes during "lighting soft" |
comment:2 by , 11 months ago
| Status: | accepted → feedback |
|---|
Hi Frank,
Thanks for reporting this problem. Do you still have the Mutated_Epitope_Schematic.cxs session file? If you do, if you open it in ChimeraX and do the same series of lighting commands (soft→simple→soft→full→soft), does it crash again?
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
comment:3 by , 11 months ago
The stack trace does not show where it crashed, but these Intel Mac's have unstable OpenGL graphics drivers and since the crash happened when switching lighting modes I would bet it crashed in Apple's Intel graphics driver. Nothing we can do about that. Apple won't fix it since they no longer make Intel Macs. Graphics on M1/M2... macs is totally stable.
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Reported by Frank Feng