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Opened 20 months ago
Closed 20 months ago
#14663 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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-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: Segmentation fault
Thread 0x0000700023c13000 (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 0x0000700022c10000 (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 0x0000700021c0d000 (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 0x0000700020c0a000 (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 0x000070001fc07000 (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 0x000070001ec04000 (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 0x000070001dc01000 (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 0x000070001cbfe000 (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 0x000070001bbfb000 (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 0x000070001abf8000 (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 0x0000700019bf5000 (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
Current thread 0x00007ff84e276700 (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":"2024-02-28 17:23:27.00 -0800","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 13.6.1 (22G313)","roots_installed":0,"name":"ChimeraX","incident_id":"040B1A16-1B2B-4397-A663-88018DE19B9F"}
{
"uptime" : 26000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 502,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,2",
"coalitionID" : 4755,
"osVersion" : {
"train" : "macOS 13.6.1",
"build" : "22G313",
"releaseType" : "User"
},
"captureTime" : "2024-02-28 17:23:20.6665 -0800",
"incident" : "040B1A16-1B2B-4397-A663-88018DE19B9F",
"pid" : 64559,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-02-28 15:39:48.3288 -0800",
"procStartAbsTime" : 19939848752521,
"procExitAbsTime" : 26066786298788,
"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":"26113322-0346-5DE8-BABE-1C4DDFA89497","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "6C1B7721-0033-A38E-9E8C-BC6A15C85694",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 6,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sleepWakeUUID" : "449A65BD-DE05-4049-A20D-23D8B4820990",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737486921704\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffea2000-7fffffea3000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000018","rawCodes":[1,24],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000018"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":64559},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737486921704\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffea2000-7fffffea3000 [ 4K] r-x\/r-x SM=SHM ",
"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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"name" : "_posixshmem.cpython-39-darwin.so"
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"name" : "nones_formathandler.cpython-39-darwin.so"
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"name" : "_version.cpython-39-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/lz4\/frame\/_frame.cpython-39-darwin.so",
"name" : "_frame.cpython-39-darwin.so"
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{
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/core\/_serialize.cpython-39-darwin.so",
"name" : "_serialize.cpython-39-darwin.so"
},
{
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"base" : 5039611904,
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/msgpack\/_cmsgpack.cpython-39-darwin.so",
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/numpy\/linalg\/lapack_lite.cpython-39-darwin.so",
"name" : "lapack_lite.cpython-39-darwin.so"
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"name" : "_ribbons.cpython-39-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/chimerax\/mmcif\/mmcif.cpython-39-darwin.so",
"name" : "mmcif.cpython-39-darwin.so"
},
{
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"name" : "_mmcif.cpython-39-darwin.so"
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/lxml\/etree.cpython-39-darwin.so",
"name" : "etree.cpython-39-darwin.so"
},
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"path" : "\/Applications\/ChimeraX-1.6.1.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/lxml\/_elementpath.cpython-39-darwin.so",
"name" : "_elementpath.cpython-39-darwin.so"
},
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"base" : 140703308288000,
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"path" : "\/usr\/lib\/system\/libsystem_kernel.dylib",
"name" : "libsystem_kernel.dylib"
},
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"path" : "\/usr\/lib\/system\/libsystem_pthread.dylib",
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"path" : "\/usr\/lib\/system\/libsystem_c.dylib",
"name" : "libsystem_c.dylib"
},
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"path" : "\/usr\/lib\/system\/libsystem_platform.dylib",
"name" : "libsystem_platform.dylib"
},
{
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"source" : "A",
"base" : 0,
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},
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"base" : 140703308939264,
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"name" : "CoreFoundation",
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},
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"uuid" : "b7674982-bc75-3c0e-a6de-ae0b4bc8896c",
"path" : "\/System\/Library\/Frameworks\/Foundation.framework\/Versions\/C\/Foundation",
"name" : "Foundation",
"CFBundleVersion" : "1979.102"
},
{
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"CFBundleIdentifier" : "com.apple.AppKit",
"size" : 16809984,
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"path" : "\/System\/Library\/Frameworks\/AppKit.framework\/Versions\/C\/AppKit",
"name" : "AppKit",
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},
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"uuid" : "bb4e24da-56b9-38fd-88d0-f529ba877272",
"path" : "\/System\/Library\/PrivateFrameworks\/SkyLight.framework\/Versions\/A\/SkyLight",
"name" : "SkyLight"
},
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"uuid" : "677ae7f7-158f-328b-85e2-8a960327856d",
"path" : "\/usr\/lib\/system\/libdispatch.dylib",
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},
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"name" : "HIToolbox"
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"name" : "dyld"
},
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"path" : "\/usr\/lib\/system\/libxpc.dylib",
"name" : "libxpc.dylib"
},
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"path" : "\/System\/Library\/Frameworks\/OpenGL.framework\/Versions\/A\/Libraries\/libCVMSPluginSupport.dylib",
"name" : "libCVMSPluginSupport.dylib"
}
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"sharedCache" : {
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"queue" : "com.apple.main-thread"
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},
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{
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===== Log before crash start =====
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/irizarr1/Desktop/LTGFB1 vs LTGFB3.cxs"
Log from Tue Nov 14 12:13:01 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "/Users/irizarr1/Desktop/LTGFB1 vs LTGFB3.cxs"
Log from Mon Nov 13 15:54:41 2023UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/irizarr1/Desktop/Structures/CryoEM
> Stuff/Krios/DenoisedModel/TGFB3_ISOLDE_06_ALR_19_real_space_refined_005.pdb"
> format pdb
Chain information for TGFB3_ISOLDE_06_ALR_19_real_space_refined_005.pdb #1
---
Chain | Description
A | No description available
B | No description available
> open "/Users/irizarr1/Desktop/Structures/TGFb1/Boar proTGFb1.pdb" format pdb
Boar proTGFb1.pdb title:
Crystal structure of pro-TGF β 1 [more info...]
Chain information for Boar proTGFb1.pdb #2
---
Chain | Description | UniProt
A B C D | transforming growth factor β-1 | TGFB1_PIG 1-361
Non-standard residues in Boar proTGFb1.pdb #2
---
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose
> select #2/A:0-361
2720 atoms, 2788 bonds, 3 pseudobonds, 340 residues, 2 models selected
> hide sel atoms
> hide sel cartoons
> select #2/B:1-361
2638 atoms, 2702 bonds, 4 pseudobonds, 330 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> select #2/A:0-361
2720 atoms, 2788 bonds, 3 pseudobonds, 340 residues, 2 models selected
> select #2/B:1-361
2638 atoms, 2702 bonds, 4 pseudobonds, 330 residues, 2 models selected
> select #2/C:-1-361
2744 atoms, 2814 bonds, 3 pseudobonds, 343 residues, 2 models selected
> select #2/D:0-361
2741 atoms, 2810 bonds, 3 pseudobonds, 342 residues, 2 models selected
> select :NAG
436 atoms, 444 bonds, 20 residues, 2 models selected
> select #2/A:0-361
2720 atoms, 2788 bonds, 3 pseudobonds, 340 residues, 2 models selected
> select #2/C:-1-361
2744 atoms, 2814 bonds, 3 pseudobonds, 343 residues, 2 models selected
> select add #2
10955 atoms, 11240 bonds, 13 pseudobonds, 1363 residues, 2 models selected
> select subtract #2
Nothing selected
> select add #2
10955 atoms, 11240 bonds, 13 pseudobonds, 1363 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models #2,1,0,0,43.102,0,1,0,42.672,0,0,1,78.094
> view matrix models #2,1,0,0,116.59,0,1,0,70.277,0,0,1,83.907
> view matrix models #2,1,0,0,118.19,0,1,0,66.583,0,0,1,86.533
> view matrix models #2,1,0,0,139.93,0,1,0,17.394,0,0,1,112.09
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.93718,0.23199,0.26051,117.79,-0.25942,0.96278,0.075884,0.90286,-0.23321,-0.1387,0.96248,105.84
> view matrix models
> #2,0.85831,0.30905,0.40963,105.02,-0.31297,0.94791,-0.059384,3.6642,-0.40665,-0.077232,0.91031,96.125
> view matrix models
> #2,0.78881,-0.25785,0.55794,115.43,0.24774,0.96413,0.095308,28.208,-0.5625,0.063046,0.82439,85.898
> view matrix models
> #2,-0.25365,0.94797,-0.1924,43.135,0.21084,-0.13994,-0.96745,107.38,-0.94404,-0.28596,-0.16438,115.71
> view matrix models
> #2,-0.56149,0.61228,-0.55663,52.342,0.61287,-0.14426,-0.77691,122.08,-0.55599,-0.77737,-0.29425,159.32
> view matrix models
> #2,-0.7336,0.394,-0.55371,50.504,0.37586,-0.44359,-0.81361,121.09,-0.56618,-0.80498,0.17733,141.39
> view matrix models
> #2,-0.6855,0.36378,-0.63067,57.255,0.43688,-0.48742,-0.75601,123.77,-0.58243,-0.79378,0.1752,140.16
> view matrix models
> #2,-0.63905,0.32972,-0.69491,63.579,0.48555,-0.52776,-0.69693,125.6,-0.59653,-0.78279,0.17717,138.9
> view matrix models
> #2,-0.63902,0.32976,-0.69492,63.58,0.4856,-0.5277,-0.69694,125.6,-0.59653,-0.78281,0.17708,138.91
> view matrix models
> #2,-0.67531,0.28856,-0.67873,62.31,0.43532,-0.58691,-0.68266,124.24,-0.59535,-0.75648,0.27073,134.39
> view matrix models
> #2,-0.70827,0.34397,-0.61647,56.079,0.3745,-0.55717,-0.74115,122.06,-0.59842,-0.7558,0.26581,134.38
> view matrix models
> #2,-0.6769,0.30427,-0.67024,61.341,0.42153,-0.58622,-0.69185,123.79,-0.60342,-0.75084,0.26855,133.82
> view matrix models
> #2,-0.61037,0.23418,-0.75671,70.962,0.49482,-0.63324,-0.59511,125.8,-0.61855,-0.73767,0.27063,132.42
> view matrix models
> #2,-0.74291,0.35372,-0.5683,51.894,0.34619,-0.5236,-0.77846,120.77,-0.57292,-0.77507,0.26653,136.47
> view matrix models
> #2,-0.74202,0.3518,-0.57066,52.101,0.34912,-0.52391,-0.77694,120.88,-0.5723,-0.77573,0.26593,136.55
> view matrix models
> #2,-0.77273,0.43687,-0.46048,42.974,0.21368,-0.50407,-0.83681,115.08,-0.59769,-0.74502,0.29616,133.01
> view matrix models
> #2,-0.7464,0.40942,-0.52465,47.906,0.26003,-0.54627,-0.79622,117.54,-0.6126,-0.73072,0.30128,131.48
> view matrix models
> #2,-0.75956,0.39524,-0.51658,47.337,0.2411,-0.56654,-0.78797,116.85,-0.6041,-0.72306,0.33503,130.37
> view matrix models
> #2,-0.76829,0.39117,-0.50667,46.598,0.24051,-0.55714,-0.79483,116.76,-0.5932,-0.73252,0.33396,131.35
> ui mousemode right translate
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.76829,0.39117,-0.50667,129.85,0.24051,-0.55714,-0.79483,225.55,-0.5932,-0.73252,0.33396,204.11
> select add #1
21868 atoms, 22290 bonds, 21 pseudobonds, 2024 residues, 4 models selected
> select subtract #2
10913 atoms, 11050 bonds, 8 pseudobonds, 661 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.99626,-0.044242,0.074154,-3.625,0.045883,0.99874,-0.020567,-3.2674,-0.07315,0.023892,0.99703,7.1041
> view matrix models
> #1,0.99593,-0.04683,0.077032,-3.6189,0.046239,0.99889,0.0094298,-7.4514,-0.077387,-0.0058295,0.99698,11.766
> view matrix models
> #1,0.99548,0.074003,0.059496,-17.677,-0.074913,0.9971,0.013208,8.8047,-0.058346,-0.017606,0.99814,10.621
> view matrix models
> #1,0.90081,0.43262,0.037153,-50.764,-0.43401,0.89971,0.04645,66.461,-0.013332,-0.057967,0.99823,9.9992
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.90081,0.43262,0.037153,-47.628,-0.43401,0.89971,0.04645,70.682,-0.013332,-0.057967,0.99823,13.482
> view matrix models
> #1,0.90081,0.43262,0.037153,-47.946,-0.43401,0.89971,0.04645,70.327,-0.013332,-0.057967,0.99823,12.418
> select subtract #1
Nothing selected
> ui mousemode right zoom
> align #2 toAtoms #1
Unequal number of atoms to pair, 10955 and 10913
> fitmap #2 to #1
Expected a keyword
> ui tool show "Show Sequence Viewer"
> sequence chain #1/A
Alignment identifier is 1/A
> sequence chain #1/B
Alignment identifier is 1/B
> fitmap #2 to #1
Expected a keyword
> select
> #1/A:33-50,67-77,96-99,126-128,136-145,205-213,215-217,324-328,358-368
1218 atoms, 1217 bonds, 74 residues, 1 model selected
> select add #1
10913 atoms, 11050 bonds, 8 pseudobonds, 661 residues, 2 models selected
> select subtract #1
Nothing selected
> select
> #1/B:33-50,67-86,96-99,137-145,180-182,205-213,272-274,361-363,365-368
1195 atoms, 1195 bonds, 73 residues, 1 model selected
> select
> #1/A:104-109,129-132,146-155,165-173,183-192,198-203,221-225,277-282,377-380,386-391,396-401,409-412
1305 atoms, 1309 bonds, 76 residues, 1 model selected
> select
> #1/A:33-50,67-77,96-99,126-128,136-145,205-213,215-217,324-328,358-368
1218 atoms, 1217 bonds, 74 residues, 1 model selected
> select add #1
10913 atoms, 11050 bonds, 8 pseudobonds, 661 residues, 2 models selected
> select subtract #1
Nothing selected
> ui mousemode right translate
> set bgColor white
> lighting simple
> graphics silhouettes true
> select add #1
10913 atoms, 11050 bonds, 8 pseudobonds, 661 residues, 2 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #1,0.90065,0.43309,0.035687,-47.785,-0.43437,0.89962,0.044776,70.619,-0.012713,-0.055829,0.99836,12.024
> view matrix models
> #1,0.89909,0.43766,0.0099126,-44.657,-0.43777,0.8989,0.018078,74.848,-0.00099829,-0.020593,0.99979,5.4134
> view matrix models
> #1,0.90016,0.43471,0.027127,-46.766,-0.43547,0.89949,0.035886,72.008,-0.0088006,-0.044116,0.99899,9.8025
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.90016,0.43471,0.027127,-45.183,-0.43547,0.89949,0.035886,73.21,-0.0088006,-0.044116,0.99899,9.5743
> save "/Users/irizarr1/Desktop/LTGFB1 vs LTGFB3.cxs"
——— End of log from Mon Nov 13 15:54:41 2023 ———
opened ChimeraX session
> select subtract #1
Nothing selected
> lighting simple
> lighting flat
> graphics silhouettes false
> graphics silhouettes true
> lighting simple
> lighting flat
> lighting soft
> lighting simple
> graphics silhouettes false
> set bgColor gray
> set bgColor white
> set bgColor black
> graphics silhouettes true
> graphics silhouettes false
> lighting soft
> ui mousemode right select
Drag select of 34 atoms, 36 bonds
> select clear
Drag select of 42 atoms, 43 bonds
> hide sel atoms
> save "/Users/irizarr1/Desktop/LTGFB1 vs LTGFB3.cxs"
——— End of log from Tue Nov 14 12:13:01 2023 ———
opened ChimeraX session
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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
OpenGL version: 4.1 INTEL-20.6.4
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: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.6.1 (22G313)
Kernel Version: Darwin 22.6.0
Time since boot: 1 day, 18 hours, 38 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: 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-Clipper: 0.21.0
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-ISOLDE: 1.6.0
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 , 20 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Window Toolkit |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 |
comment:2 by , 20 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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