![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#10034 closed defect (nonchimerax)
Graphics crash, macOS 13.3.1, Intel Iris Plus Graphics
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff85ae90340 (most recent call first):
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2730 in draw_elements
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1736 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 836 in _draw_geometry
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 771 in draw_self
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 764 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1551 in _draw_multiple
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1538 in draw_opaque
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1563 in draw_depth
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 1438 in use_shadow_map
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 609 in _compute_shadowmaps
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 215 in _draw_scene
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 158 in update_graphics_now
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/graphics.py", line 145 in resizeEvent
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/graphics.py", line 57 in event
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-10-19 14:39:15.00 -0700","app_version":"1.5.0","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.5.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.3.1 (22E772610a)","roots_installed":0,"name":"ChimeraX","incident_id":"D1DDD697-46DE-49FE-8A59-0F41FFF7F490"}
{
"uptime" : 210000,
"procRole" : "Background",
"version" : 2,
"userID" : 717840800,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 654,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E772610a",
"releaseType" : "User"
},
"captureTime" : "2023-10-19 14:39:08.4683 -0700",
"incident" : "D1DDD697-46DE-49FE-8A59-0F41FFF7F490",
"pid" : 1043,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-10-06 09:11:40.0687 -0700",
"procStartAbsTime" : 104145665444,
"procExitAbsTime" : 215094019052567,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.5.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.5.0","CFBundleVersion":"1.5.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C93DC040-943C-5149-87F2-478370A25C24","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "BAE0E020-898D-4407-F6C8-554453687944",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 12477,
"bridgeVersion" : {"build":"20P4252","train":"7.4"},
"sleepWakeUUID" : "D85E25F6-7479-4776-A6C3-702E4EE84ABA",
"sip" : "enabled",
"vmRegionInfo" : "0xd316c6400 is not in any region. Bytes after previous region: 51128730625 Bytes before following region: 105496452504576\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 1438a3000-149e9e000 [102.0M] r--\/rwx SM=COW ...t_id=88be399f\n---> GAP OF 0x5ffeb6162000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000000d316c6400","rawCodes":[1,56663761920],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000d316c6400"},
"vmregioninfo" : "0xd316c6400 is not in any region. Bytes after previous region: 51128730625 Bytes before following region: 105496452504576\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n mapped file 1438a3000-149e9e000 [102.0M] r--\/rwx SM=COW ...t_id=88be399f\n---> GAP OF 0x5ffeb6162000 BYTES\n MALLOC_NANO 600000000000-600008000000 [128.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.1G resident=0K(0%) swapped_out_or_unallocated=1.1G(100%)\nWritable regions: Total=1.2G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.2G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 384K 3 \nActivity Tracing 256K 1 \nCG backing stores 5232K 9 \nCG image 484K 41 \nColorSync 268K 29 \nCoreAnimation 200K 34 \nCoreGraphics 20K 4 \nCoreUI image data 5220K 44 \nFoundation 16K 1 \nKernel Alloc Once 8K 1 \nMALLOC 884.1M 659 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMach message 16K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 120K 30 \nStack 158.2M 31 \nStack Guard 56.0M 1 \nVM_ALLOCATE 135.7M 138 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 824 1 \n__DATA 46.1M 740 \n__DATA_CONST 39.8M 379 \n__DATA_DIRTY 1786K 219 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 201.2M 139 \n__OBJC_RO 66.2M 1 \n__OBJC_RW 2012K 2 \n__TEXT 917.5M 741 \ndyld private memory 420K 4 \nmapped file 221.2M 58 \nshared memory 3172K 40 \n=========== ======= ======= \nTOTAL 2.7G 3369 \nTOTAL, minus reserved VM space 2.7G 3369 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "CrBrowserMain",
"queue" : "com.apple.main-thread"
}
},
"logWritingSignature" : "c225b0961fa7c5b0e10a9393376ebe663c17f89c",
"trialInfo" : {
"rollouts" : [
{
"rolloutId" : "63508950b3714d3622fc77f7",
"factorPackIds" : {
"SIRI_MEMORY_SYNC_CONFIG" : "63508beab3714d3622fc7808"
},
"deploymentId" : 240000004
},
{
"rolloutId" : "5ffde50ce2aacd000d47a95f",
"factorPackIds" : {
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}
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure
> Files/Ab regions_GDIR_Glycans selected.cxs" format session
> set bgColor #ffffff00
opened ChimeraX session
> select
> /A,E-F:35-40,45-47,53-55,83-85,91-94,130-133,154-162,169-177,181-183,191-193,201-203,216-218,223-228,236-239,242-245,271-273,284-287,294-298,304-312,315-320,330-334,358-362,374-378,381-385,413-421,433-435,443-447,451-456,465-470,486-491,494-499
3780 atoms, 3801 bonds, 459 residues, 1 model selected
> select /A,E-F:330
30 atoms, 30 bonds, 3 residues, 1 model selected
> select /A,E-F:330
30 atoms, 30 bonds, 3 residues, 1 model selected
> style sel stick
Changed 30 atom styles
> hide sel surfaces
> color (#!1 & sel) red
> color (#!1 & sel) orange
> select CDRH1
204 atoms, 207 bonds, 27 residues, 1 model selected
> select CDRH3
636 atoms, 663 bonds, 75 residues, 1 model selected
> open /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta
Failed opening file /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta:
Sequence '7KDE_2|Chains D[auth E], E[auth F], F[auth G]|Envelope glycoprotein
gp120|Human immunodeficiency virus 1 (11676)' differs in length from preceding
sequences, and it is therefore impossible to open these sequences as an
alignment. If you want to open the sequences individually, specify 'false' as
the value of the 'alignment' keyword in the 'open' command.
> open /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta
Failed opening file /Users/kmckenney/Downloads/rcsb_pdb_7KDE.fasta:
Sequence '7KDE_2|Chains D[auth E], E[auth F], F[auth G]|Envelope glycoprotein
gp120|Human immunodeficiency virus 1 (11676)' differs in length from preceding
sequences, and it is therefore impossible to open these sequences as an
alignment. If you want to open the sequences individually, specify 'false' as
the value of the 'alignment' keyword in the 'open' command.
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
> open "/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure
> Files/Ab regions_GDIR_Glycans selected.cxs"
Log from Fri Aug 11 13:14:59 2023UCSF ChimeraX version: 1.5 (2022-11-24)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/kmckenney/Desktop/Infant bNAbs/EM/Original EM Files/High res
> CP20.2_J198_C3_5_real_space_refined_012.pdb"
Chain information for High res CP20.2_J198_C3_5_real_space_refined_012.pdb #1
---
Chain | Description
A E F | No description available
B G I | No description available
C J K | No description available
D M N | No description available
H O P | No description available
L Q R | No description available
> set bgColor white
> select /E/F/B/G/I/C/J/K/D/M/N/O/P/Q/R
19512 atoms, 20022 bonds, 13 pseudobonds, 2475 residues, 2 models selected
> hide sel atoms
> select /A
3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected
> select /H/L
1819 atoms, 1870 bonds, 240 residues, 1 model selected
> style sel stick
Changed 1819 atom styles
> hide sel atoms
> select /A
3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected
> select /A
3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected
> style sel stick
Changed 3776 atom styles
> ui mousemode right select
Drag select of 584 atoms, 2 pseudobonds, 601 bonds
> hide sel atoms
Drag select of 7 atoms, 5 bonds
> hide sel atoms
Drag select of 384 atoms, 381 bonds
> hide sel atoms
Drag select of 136 atoms, 130 bonds
> hide sel atoms
Drag select of 416 atoms, 434 bonds
> hide sel atoms
Drag select of 2 atoms, 1 bonds
> hide sel atoms
Drag select of 1 atoms, 1 bonds
> hide sel atoms
Drag select of 11 atoms, 10 bonds
> hide sel atoms
Drag select of 11 atoms, 8 bonds
> hide sel atoms
Drag select of 5 atoms, 3 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
> select clear
Drag select of 125 atoms, 134 bonds
> name frozen N332 sel
Drag select of 469 atoms, 1 pseudobonds, 474 bonds
> hide sel atoms
Drag select of 207 atoms, 209 bonds
> hide sel atoms
Drag select of 4 atoms, 3 bonds
> hide sel atoms
Drag select of 119 atoms, 109 bonds
> hide sel atoms
Drag select of 3 atoms, 3 bonds
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 1 atoms
> hide sel atoms
Drag select of 11 atoms, 8 bonds
> hide sel atoms
Drag select of 33 atoms, 34 bonds
> name frozen N156 sel
> select /A
3776 atoms, 3886 bonds, 6 pseudobonds, 459 residues, 3 models selected
> show sel atoms
> show sel surfaces
> color (#!1 & sel) light gray
> select clear
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> color (#!1 & sel) blue
> select N156
33 atoms, 34 bonds, 3 residues, 1 model selected
> color (#!1 & sel) blue
> style sel stick
Changed 33 atom styles
> hide sel surfaces
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> hide sel surfaces
> select /A:448@OD1
1 atom, 1 residue, 1 model selected
> undo
[Repeated 4 time(s)]
> select /A
3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected
> show sel surfaces
> select /H/L
1819 atoms, 1870 bonds, 240 residues, 1 model selected
> show sel atoms
> ui tool show "Show Sequence Viewer"
> sequence chain /A /E /F
Alignment identifier is 1
> sequence chain /H /O /P
Alignment identifier is 2
> sequence chain /L /Q /R
Alignment identifier is 3
> select /H,O-P:1
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /H,O-P:1-26
534 atoms, 537 bonds, 78 residues, 1 model selected
> select /H,O-P:1
27 atoms, 24 bonds, 3 residues, 1 model selected
> select /H,O-P:1-25
522 atoms, 525 bonds, 75 residues, 1 model selected
> name frozen FWR1-HC sel
> select /H,O-P:26
12 atoms, 9 bonds, 3 residues, 1 model selected
> select /H,O-P:26-34
204 atoms, 207 bonds, 27 residues, 1 model selected
> name frozen CDRH1 sel
> select /H,O-P:35
42 atoms, 45 bonds, 3 residues, 1 model selected
> select /H,O-P:35-50
420 atoms, 438 bonds, 51 residues, 1 model selected
> name frozen FWR2-HC sel
> select /H,O-P:51
24 atoms, 21 bonds, 3 residues, 1 model selected
> select /H,O-P:51-57
165 atoms, 168 bonds, 21 residues, 1 model selected
> name frozen CDRH2 sel
> select /H,O-P:58
33 atoms, 33 bonds, 3 residues, 1 model selected
> select /H,O-P:58-92
918 atoms, 936 bonds, 114 residues, 1 model selected
> name frozen FWR3-HC sel
> select /H,O-P:93-94
48 atoms, 45 bonds, 6 residues, 1 model selected
> select /H,O-P:93-102
636 atoms, 663 bonds, 75 residues, 1 model selected
> name frozen CDRH3 sel
> select /H,O-P:103
42 atoms, 45 bonds, 3 residues, 1 model selected
> select /H,O-P:103-112
219 atoms, 222 bonds, 30 residues, 1 model selected
> name frozen FWR4-HC sel
> select /L,Q-R:3-4
45 atoms, 42 bonds, 6 residues, 1 model selected
> select /L,Q-R:3-26
462 atoms, 468 bonds, 69 residues, 1 model selected
> name frozen FWR1-LC sel
> select /L,Q-R:27-27A
66 atoms, 63 bonds, 9 residues, 1 model selected
> select /L,Q-R:27-32
162 atoms, 159 bonds, 24 residues, 1 model selected
> name frozen CDRL1 sel
> select /L,Q-R:33
21 atoms, 18 bonds, 3 residues, 1 model selected
> select /L,Q-R:33-49
414 atoms, 429 bonds, 51 residues, 1 model selected
> name frozen FWR2-LC sel
> select /L,Q-R:50
18 atoms, 15 bonds, 3 residues, 1 model selected
> select /L,Q-R:50-52
66 atoms, 63 bonds, 9 residues, 1 model selected
> name frozen CDRL2 sel
> select /L,Q-R:53-54
60 atoms, 57 bonds, 6 residues, 1 model selected
> select /L,Q-R:53-88
783 atoms, 795 bonds, 108 residues, 1 model selected
> name frozen FWR3-LC sel
> select /L,Q-R:89-90
30 atoms, 27 bonds, 6 residues, 1 model selected
> select /L,Q-R:89-97
279 atoms, 288 bonds, 36 residues, 1 model selected
> name frozen CDRL3 sel
> select /L,Q-R:98-99
45 atoms, 45 bonds, 6 residues, 1 model selected
> select /L,Q-R:98-106A
207 atoms, 207 bonds, 30 residues, 1 model selected
> name frozen FWR4-LC sel
> select /A,E-F:324-325
36 atoms, 33 bonds, 6 residues, 1 model selected
> select /A,E-F:324-327
93 atoms, 90 bonds, 12 residues, 1 model selected
> name frozen GDIR sel
> save "/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure
> Files/Ab regions_GDIR_Glycans selected.cxs"
> select /H
1028 atoms, 1060 bonds, 131 residues, 1 model selected
> color sel magenta
> show sel cartoons
> hide sel atoms
> select /L
791 atoms, 810 bonds, 109 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select clear
> select GDIR
3437 atoms, 90 bonds, 436 residues, 1 model selected
> select N156
33 atoms, 34 bonds, 3 residues, 1 model selected
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> select CDRH3
636 atoms, 663 bonds, 75 residues, 1 model selected
> select FWR3-LC
783 atoms, 795 bonds, 108 residues, 1 model selected
> select FWR4-LC
207 atoms, 207 bonds, 30 residues, 1 model selected
> select GDIR
3437 atoms, 90 bonds, 436 residues, 1 model selected
> select /A,E-F:324
12 atoms, 9 bonds, 3 residues, 1 model selected
> select /A,E-F:324-327
93 atoms, 90 bonds, 12 residues, 1 model selected
> hide sel surfaces
> name frozen GDIR_2 sel
> select GDIR
3437 atoms, 90 bonds, 436 residues, 1 model selected
> select GDIR_2
3437 atoms, 90 bonds, 436 residues, 1 model selected
> select CDRL3
279 atoms, 288 bonds, 36 residues, 1 model selected
> select clear
> select /A,E-F:324
12 atoms, 9 bonds, 3 residues, 1 model selected
> select /A,E-F:324-327
93 atoms, 90 bonds, 12 residues, 1 model selected
> color (#!1 & sel) lime
> show sel surfaces
> hide sel surfaces
> select /L
791 atoms, 810 bonds, 109 residues, 1 model selected
> select /A
3776 atoms, 3886 bonds, 5 pseudobonds, 459 residues, 2 models selected
> show sel surfaces
> select clear
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> color (#!1 & sel) blue
> show sel surfaces
[Repeated 1 time(s)]
> select clear
[Repeated 1 time(s)]
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> show sel surfaces
> select N156
33 atoms, 34 bonds, 3 residues, 1 model selected
> show sel surfaces
> hide sel atoms
> show sel surfaces
> show sel atoms
> show sel cartoons
> show sel surfaces
> style sel sphere
Changed 33 atom styles
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> style sel sphere
Changed 125 atom styles
> select clear
> save "/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure
> Files/JPEG/V2 Figs/Fig 4b.jpg" width 864 height 598 supersample 3
> select ::name="BMA"::name="MAN"::name="NAG"
1329 atoms, 1371 bonds, 102 residues, 1 model selected
> style sel sphere
Changed 1329 atom styles
> select clear
> save "/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure
> Files/JPEG/V2 Figs/Fig 4b.jpg" width 864 height 598 supersample 3
> select N332
125 atoms, 134 bonds, 12 residues, 1 model selected
> style sel stick
Changed 125 atom styles
> select /A,E-F:324
12 atoms, 9 bonds, 3 residues, 1 model selected
> select /A,E-F:324-327
93 atoms, 90 bonds, 12 residues, 1 model selected
> style sel stick
Changed 93 atom styles
> style sel stick
Changed 93 atom styles
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> select N156
33 atoms, 34 bonds, 3 residues, 1 model selected
> style sel stick
Changed 33 atom styles
> select CDRH3
636 atoms, 663 bonds, 75 residues, 1 model selected
> show sel atoms
> select clear
> hide atoms
> undo
Drag select of 212 atoms
> hide sel atoms
[Repeated 1 time(s)]Drag select of 212 atoms
> hide sel atoms
> ui mousemode right "translate selected models"
> view matrix models #1,1,0,0,17.322,0,1,0,-36.04,0,0,1,-18.007
> view matrix models #1,1,0,0,25.96,0,1,0,-52.434,0,0,1,-28.503
> select /A,E-F:324-325
36 atoms, 33 bonds, 6 residues, 1 model selected
> select /A,E-F:324-327
93 atoms, 90 bonds, 12 residues, 1 model selected
> show sel atoms
> save "/Users/kmckenney/Desktop/CP020 Paper/CP020 Paper EM/Katie Files/Figure
> Files/Ab regions_GDIR_Glycans selected.cxs"
——— End of log from Fri Aug 11 13:14:59 2023 ———
opened ChimeraX session
OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
Processor Name: Quad-Core Intel Core i7
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 512 KB
L3 Cache: 8 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
OS Loader Version: 577~129
Software:
System Software Overview:
System Version: macOS 13.3.1 (a) (22E772610a)
Kernel Version: Darwin 22.4.0
Time since boot: 14 days, 3 hours, 15 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)
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
HP E27 G5:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: CNC3011BB8
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.55
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.1.0
Babel: 2.11.0
backcall: 0.2.0
blockdiag: 3.0.0
build: 0.8.0
certifi: 2021.10.8
cftime: 1.6.2
charset-normalizer: 2.1.1
ChimeraX-AddCharge: 1.4
ChimeraX-AddH: 2.2.1
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.6
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.41.5
ChimeraX-AtomicLibrary: 8.0.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3
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: 2.7.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.1
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.2
ChimeraX-CommandLine: 1.2.4
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.5
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.3
ChimeraX-DockPrep: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 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: 1.1.2
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.1
ChimeraX-MatchMaker: 2.0.9
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.8
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.6
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.1
ChimeraX-MouseModes: 1.1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.9.1
ChimeraX-PDB: 2.6.8
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-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.7.2
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
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.1.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.24.3
ChimeraX-uniprot: 2.2.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.1.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.1
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0.1
colorama: 0.4.5
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.32
debugpy: 1.6.4
decorator: 5.1.1
docutils: 0.19
entrypoints: 0.4
executing: 1.2.0
filelock: 3.7.1
fonttools: 4.38.0
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.33
imagecodecs: 2022.7.31
imagesize: 1.4.1
importlib-metadata: 5.1.0
ipykernel: 6.15.3
ipython: 8.4.0
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.1.2
jupyter-client: 7.3.4
jupyter-core: 5.1.0
kiwisolver: 1.4.4
line-profiler: 3.5.1
lxml: 4.9.1
lz4: 4.0.2
MarkupSafe: 2.1.1
matplotlib: 3.5.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.0
networkx: 2.8.5
numexpr: 2.8.4
numpy: 1.23.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.2.0
pip: 22.2.2
pkginfo: 1.8.3
platformdirs: 2.5.4
prompt-toolkit: 3.0.33
psutil: 5.9.1
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.12.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2022.6
pyzmq: 24.0.1
qtconsole: 5.3.1
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.1
scipy: 1.9.0
setuptools: 65.1.1
setuptools-scm: 7.0.5
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 5.1.1
sphinx-autodoc-typehints: 1.19.1
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tifffile: 2022.7.31
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.3.0
typing-extensions: 4.4.0
urllib3: 1.26.13
wcwidth: 0.2.5
webcolors: 1.12
wheel: 0.37.1
wheel-filename: 1.4.1
zipp: 3.11.0
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 → Crash in drawing code |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Crash in drawing code → Graphics crash, macOS 13.3.1, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.