![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9506 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: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x000070000f9cc000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 316 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 574 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 1297 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001b9f0000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001a9ed000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000199ea000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000189e7000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000179e4000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000169e1000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000159de000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000149db000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000139d8000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000129d5000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007000119d2000 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007ff84dbc6340 (most recent call first):
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX-1.6.1.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":"2023-08-02 15:39:07.00 -0700","app_version":"1.6.1","slice_uuid":"5df621ee-554e-36a8-b448-93b2334e5480","build_version":"1.6.1.0","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":"06F37F7C-530B-4894-8CD6-400FFB472B89"}
{
"uptime" : 160000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 16874,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E772610a",
"releaseType" : "User"
},
"captureTime" : "2023-08-02 15:39:01.4054 -0700",
"incident" : "06F37F7C-530B-4894-8CD6-400FFB472B89",
"pid" : 33566,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-02 14:58:03.2902 -0700",
"procStartAbsTime" : 158997330023369,
"procExitAbsTime" : 161455344135545,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.6.1","CFBundleVersion":"1.6.1.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"F3B4DDE6-BA5D-596A-A42F-5231E3159F31","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "53E5FCD2-F51A-5F42-7302-AA67B2C67DD8",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 5683,
"bridgeVersion" : {"build":"20P4252","train":"7.4"},
"sleepWakeUUID" : "C8D8C518-BD44-4EC4-9400-87DE26087AFC",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000002\n"],
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 4,
"threads" : 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"arch" : "x86_64",
"base" : 140703300165632,
"size" : 557048,
"uuid" : "0773ddbc-707e-3b56-ad3e-97aaa9b2c3ed",
"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140703301750784,
"size" : 40944,
"uuid" : "c99e2bcf-5fa3-3690-9f4b-5e9a08b57343",
"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
"size" : 0,
"source" : "A",
"base" : 0,
"uuid" : "00000000-0000-0000-0000-000000000000"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140707865653248,
"size" : 45048,
"uuid" : "bb3d3302-9d3a-37a6-99ce-d7913139f33c",
"path" : "\/System\/Library\/PrivateFrameworks\/GPUSupport.framework\/Versions\/A\/Libraries\/libGPUSupportMercury.dylib",
"name" : "libGPUSupportMercury.dylib"
},
{
"source" : "P",
"arch" : "x86_64",
"base" : 140712225075200,
"CFBundleShortVersionString" : "20.5.7",
"CFBundleIdentifier" : "com.apple.driver.AppleIntelICLGraphicsGLDriver",
"size" : 15859712,
"uuid" : "360970db-acdd-3d87-8f92-3df8c3e8fd61",
"path" : "\/System\/Library\/Extensions\/AppleIntelICLGraphicsGLDriver.bundle\/Contents\/MacOS\/AppleIntelICLGraphicsGLDriver",
"name" : "AppleIntelICLGraphicsGLDriver",
"CFBundleVersion" : "20.0.5"
}
],
"sharedCache" : {
"base" : 140703297417216,
"size" : 21474836480,
"uuid" : "5dd9a20c-1502-31aa-84b0-1cda4c95765b"
},
"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 256K 2 \nActivity Tracing 256K 1 \nCG backing stores 15.1M 9 \nCG image 1840K 75 \nColorSync 260K 29 \nCoreAnimation 3956K 140 \nCoreGraphics 16K 3 \nCoreImage 24K 2 \nCoreServices 624K 2 \nCoreUI image data 5384K 39 \nFoundation 32K 2 \nIOKit 15.5M 2 \nKernel Alloc Once 8K 1 \nMALLOC 713.7M 819 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 640K 2 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 24K 4 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.2M 43 \nStack 357.8M 43 \nVM_ALLOCATE 170.6M 173 \n__CTF 824 1 \n__DATA 47.3M 773 \n__DATA_CONST 41.3M 401 \n__DATA_DIRTY 1812K 230 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 201.6M 150 \n__OBJC_RO 66.2M 1 \n__OBJC_RW 2012K 2 \n__TEXT 947.9M 778 \ndyld private memory 292K 4 \nmapped file 569.5M 94 \nshared memory 3520K 32 \n=========== ======= ======= \nTOTAL 3.4G 3873 \nTOTAL, minus reserved VM space 3.2G 3873 \n",
"legacyInfo" : {
"threadTriggered" : {
"name" : "Chrome_InProcGpuThread"
}
},
"logWritingSignature" : "1049d502231b9b4e3cbbc90dd1c1bc0d560cbd17",
"trialInfo" : {
"rollouts" : [
{
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"factorPackIds" : {
},
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},
{
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"factorPackIds" : {
},
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}
],
"experiments" : [
{
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"experimentId" : "64a844035c85000c0f42398a",
"deploymentId" : 400000016
},
{
"treatmentId" : "3a3cf641-8471-4e4e-9ad4-81d0ede970fd",
"experimentId" : "64a84dae90d82611a0bd7d3d",
"deploymentId" : 400000010
}
]
}
}
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF 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/jon/Dropbox (Scripps Research)/Foundry/Foundry
> (1)/NA/Immunogen/Ind11_N2_S245N_initial_model_tetramer.pdb"
Chain information for Ind11_N2_S245N_initial_model_tetramer.pdb #1
---
Chain | Description
A C D E | No description available
> set bgColor white
> hide cartoons
> show cartoons
> show atoms
> hide atoms
> color #1 silver
> color #1 darkgrey
> lighting soft
> lighting full
> lighting simple
> lighting soft
> select #0 D
Expected a keyword
> select #0:D
Nothing selected
> select #0/A
Nothing selected
> select #0/a
Nothing selected
> select #0:/a
Expected an objects specifier or a keyword
> select #0 /a
Nothing selected
> select #0 /A
Nothing selected
> select #0/A
Nothing selected
> select /A
3099 atoms, 3126 bonds, 6 pseudobonds, 444 residues, 2 models selected
> select #1/A
3099 atoms, 3126 bonds, 6 pseudobonds, 444 residues, 2 models selected
> color #1 #919191ff
> color #1 silver
> color #1 #73fa79ff
> color #1 silver
> color (#!1 & sel) #009051ff
> color (#!1 & sel) #919191ff
> color (#!1 & sel) #797979ff
> color (#!1 & sel) #5e5e5eff
> color (#!1 & sel) #797979ff
> select clear
> color #a9a9a9ff
> color #c0c0c0ff
> select #1/B
61 atoms, 65 bonds, 5 residues, 1 model selected
> select #1/A
3099 atoms, 3126 bonds, 6 pseudobonds, 444 residues, 2 models selected
> color (#!1 & sel) #797979ff
> select #1/C
3099 atoms, 3126 bonds, 444 residues, 1 model selected
> color sel #919191ff
> color sel #797979ff
> select clear
> select #1/C 88
Expected a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C /D /E
Alignment identifier is 1
> select /A,C-E:86
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:86
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel #fffb00ff
> style sel stick
Changed 32 atom styles
> color sel byhetero
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> set bgColor gray
> set bgColor black
> set bgColor white
> select /A,C-E:104-109,142-146
332 atoms, 328 bonds, 44 residues, 1 model selected
> select /A,C-E:104
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:104
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select clear
> select /A,C-E:146
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:146-147
64 atoms, 60 bonds, 8 residues, 1 model selected
> select /A,C-E:141-142
64 atoms, 60 bonds, 8 residues, 1 model selected
> select /A,C-E:141-142
64 atoms, 60 bonds, 8 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:104-109,142-146
332 atoms, 328 bonds, 44 residues, 1 model selected
> select /A,C-E:146
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:146
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:199
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:199
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:201
20 atoms, 16 bonds, 4 residues, 1 model selected
> select /A,C-E:200-201
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A,C-E:200-201
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A,C-E:200-201
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A,C-E:200
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:200
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #ff2600ff
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:208
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:208
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:234
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:234
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:245
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:245
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel #ff2600ff
> color sel #fffb00ff
> color sel byhetero
> select /A,C-E:306
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:306
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:329
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A,C-E:329
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:342
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:342
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #ff40ffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:358
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:358
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:367
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:367
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #fffb00ff
> color sel #ff2600ff
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #ff40ffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:384-385
60 atoms, 56 bonds, 8 residues, 1 model selected
> select /A,C-E:386
20 atoms, 16 bonds, 4 residues, 1 model selected
> select /A,C-E:385-386
56 atoms, 52 bonds, 8 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select clear
> save "/Users/jon/Dropbox (Scripps Research)/Foundry/Foundry
> (1)/NA/Immunogen/Ind11_N2_S245N_Hyperglycosylation.cxs"
> save Ind11_S245N_Hyperglycosylation_all_TOP.tiff supersample 8
> transparentBackground
Missing "transparentBackground" keyword's argument
> true
Unknown command: true
> save Ind11_S245N_Hyperglycosylation_all_TOP.tiff supersample 8
> transparentBackground Backgroundtrue
Invalid "transparentBackground" argument: Expected true or false (or 1 or 0)
> save Ind11_S245N_Hyperglycosylation_all_TOP.tiff supersample 8
> transparentBackground Background true
Invalid "transparentBackground" argument: Expected true or false (or 1 or 0)
> save /Users/jontorres/Desktop/Ind11_S245N_Hyperglycosylation_all_TOP.tiff
> supersample 8
Invalid "supersample" argument: Expected an integer
No map chosen to save
> save /Users/jontorres/Desktop/Ind11_S245N_Hyperglycosylation_all_TOP.tiff
> supersample
Missing "supersample" keyword's argument
> save /Users/jontorres/Desktop/Ind11_S245N_Hyperglycosylation_all_TOP.tiff
> supersample transparentBackground true
Invalid "supersample" argument: Expected an integer
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/jon/Dropbox (Scripps Research)/Foundry/Foundry
> (1)/NA/Immunogen/Ind11_N2_S245N_Hyperglycosylation.cxs"
Log from Wed Aug 2 15:27:46 2023 Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF 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/jon/Dropbox (Scripps Research)/Foundry/Foundry
> (1)/NA/Immunogen/Ind11_N2_S245N_initial_model_tetramer.pdb"
Chain information for Ind11_N2_S245N_initial_model_tetramer.pdb #1
---
Chain | Description
A C D E | No description available
> set bgColor white
> hide cartoons
> show cartoons
> show atoms
> hide atoms
> color #1 silver
> color #1 darkgrey
> lighting soft
> lighting full
> lighting simple
> lighting soft
> select #0 D
Expected a keyword
> select #0:D
Nothing selected
> select #0/A
Nothing selected
> select #0/a
Nothing selected
> select #0:/a
Expected an objects specifier or a keyword
> select #0 /a
Nothing selected
> select #0 /A
Nothing selected
> select #0/A
Nothing selected
> select /A
3099 atoms, 3126 bonds, 6 pseudobonds, 444 residues, 2 models selected
> select #1/A
3099 atoms, 3126 bonds, 6 pseudobonds, 444 residues, 2 models selected
> color #1 #919191ff
> color #1 silver
> color #1 #73fa79ff
> color #1 silver
> color (#!1 & sel) #009051ff
> color (#!1 & sel) #919191ff
> color (#!1 & sel) #797979ff
> color (#!1 & sel) #5e5e5eff
> color (#!1 & sel) #797979ff
> select clear
> color #a9a9a9ff
> color #c0c0c0ff
> select #1/B
61 atoms, 65 bonds, 5 residues, 1 model selected
> select #1/A
3099 atoms, 3126 bonds, 6 pseudobonds, 444 residues, 2 models selected
> color (#!1 & sel) #797979ff
> select #1/C
3099 atoms, 3126 bonds, 444 residues, 1 model selected
> color sel #919191ff
> color sel #797979ff
> select clear
> select #1/C 88
Expected a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain /A /C /D /E
Alignment identifier is 1
> select /A,C-E:86
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:86
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel #fffb00ff
> style sel stick
Changed 32 atom styles
> color sel byhetero
> select clear
> lighting soft
> lighting full
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> graphics silhouettes true
> graphics silhouettes false
> set bgColor gray
> set bgColor black
> set bgColor white
> select /A,C-E:104-109,142-146
332 atoms, 328 bonds, 44 residues, 1 model selected
> select /A,C-E:104
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:104
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select clear
> select /A,C-E:146
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:146-147
64 atoms, 60 bonds, 8 residues, 1 model selected
> select /A,C-E:141-142
64 atoms, 60 bonds, 8 residues, 1 model selected
> select /A,C-E:141-142
64 atoms, 60 bonds, 8 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:104-109,142-146
332 atoms, 328 bonds, 44 residues, 1 model selected
> select /A,C-E:146
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:146
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:199
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:199
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:201
20 atoms, 16 bonds, 4 residues, 1 model selected
> select /A,C-E:200-201
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A,C-E:200-201
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A,C-E:200-201
52 atoms, 48 bonds, 8 residues, 1 model selected
> select /A,C-E:200
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:200
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #ff2600ff
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:208
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:208
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:234
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:234
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:245
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:245
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> color sel #ff2600ff
> color sel #fffb00ff
> color sel byhetero
> select /A,C-E:306
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:306
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:329
24 atoms, 20 bonds, 4 residues, 1 model selected
> select /A,C-E:329
24 atoms, 20 bonds, 4 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:342
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:342
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #ff40ffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:358
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:358
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:367
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:367
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #fffb00ff
> color sel #ff2600ff
> color sel #fffb00ff
> show sel atoms
> color sel byhetero
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:419
32 atoms, 28 bonds, 4 residues, 1 model selected
> color sel #ff40ffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:393
32 atoms, 28 bonds, 4 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:384-385
60 atoms, 56 bonds, 8 residues, 1 model selected
> select /A,C-E:386
20 atoms, 16 bonds, 4 residues, 1 model selected
> select /A,C-E:385-386
56 atoms, 52 bonds, 8 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> select /A,C-E:385
36 atoms, 32 bonds, 4 residues, 1 model selected
> color sel #00fdffff
> color sel #00f900ff
> show sel atoms
> color sel byhetero
> select clear
> save "/Users/jon/Dropbox (Scripps Research)/Foundry/Foundry
> (1)/NA/Immunogen/Ind11_N2_S245N_Hyperglycosylation.cxs"
——— End of log from Wed Aug 2 15:27:46 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 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro16,2
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: 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, 5 hours, 2 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: No
Connection Type: Internal
LG UltraFine:
Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 909NTTQBE673
Mirror: Off
Online: Yes
Rotation: Supported
Automatically Adjust Brightness: Yes
Connection Type: Thunderbolt/DisplayPort
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 13.3.1, Intel Iris Plus Graphics |
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Apple Intel graphics driver crash.