![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9347 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 0x00007000221e2000 (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 0x00007000211df000 (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 0x00007000201dc000 (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 0x000070001f1d9000 (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 0x000070001e1d6000 (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 0x000070001d1d3000 (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 0x000070001c1d0000 (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 0x000070001b1cd000 (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 0x000070001a1ca000 (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 0x00007000191c7000 (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 0x00007000181c4000 (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 0x00007ff85c99f340 (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":"2023-07-10 17:44:48.00 +0900","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":"7B98D75F-DB6F-4966-9772-5AF0650A0235"}
{
"uptime" : 370000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro15,4",
"coalitionID" : 3742,
"osVersion" : {
"train" : "macOS 13.3.1",
"build" : "22E772610a",
"releaseType" : "User"
},
"captureTime" : "2023-07-10 17:44:38.6261 +0900",
"incident" : "7B98D75F-DB6F-4966-9772-5AF0650A0235",
"pid" : 33593,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-07-10 12:28:22.3172 +0900",
"procStartAbsTime" : 360347279015342,
"procExitAbsTime" : 379303394073972,
"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":"E357CF6C-CCB5-5E88-A2E7-401919C12DDC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "40B43760-140E-6FE4-32AF-31BA87A5EF65",
"throttleTimeout" : 2147483647,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 11,
"bridgeVersion" : {"build":"20P4252","train":"7.4"},
"sleepWakeUUID" : "985DCA5A-E7D4-4135-947C-766110C63AFA",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 140737487380456\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff12000-7ffffff13000 [ 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"},
"ktriageinfo" : "VM - (arg = 0x0) Waiting on busy page was interrupted\nVM - (arg = 0x0) pmap_enter retried due to resource shortage\n",
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 140737487380456\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffff12000-7ffffff13000 [ 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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"deploymentId" : 240000010
},
{
"rolloutId" : "6112d17137f5d11121dcd4e2",
"factorPackIds" : {
},
"deploymentId" : 240000308
}
],
"experiments" : [
{
"treatmentId" : "c28e4ee6-1b08-4f90-8e05-2809e78310a3",
"experimentId" : "6317d2003d24842ff850182a",
"deploymentId" : 400000013
},
{
"treatmentId" : "8ca8349c-e2bc-482c-9ca7-3907b48a5341",
"experimentId" : "648b5a581b04c12d4127bbb6",
"deploymentId" : 400000001
}
]
}
}
===== Log before crash start =====
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
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 8gkh
Summary of feedback from opening 8gkh fetched from pdb
---
note | Fetching compressed mmCIF 8gkh from
http://files.rcsb.org/download/8gkh.cif
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #1
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #1
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> transparency /N,T,W 20 target s
> select /P:300:310:487:498:513
38 atoms, 33 bonds, 5 residues, 1 model selected
> show sel target a
> color sel byhetero
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #2
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #2
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> transparency /N,T,W 20 target s
> select /P:35:36
34 atoms, 32 bonds, 4 residues, 2 models selected
> show sel target a
> color sel byhetero
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #3
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #3
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> select /P:289:290:293-297:299-301:304:308-312:316:319-321:338-340
528 atoms, 513 bonds, 69 residues, 3 models selected
> show sel target a
> color sel byhetero
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #4
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #4
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> select /P:298:302:303:306:307:313:314:322-337
700 atoms, 700 bonds, 92 residues, 4 models selected
> show sel target a
> color sel byhetero
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #5
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #5
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> select
> /P:398:400:405:406:408:409:444:446:448:452:453:456:457:459:462:463:466-469:471:476:478:480:483:485:486:409:419:494:405:497:508:528:538:614:615
1365 atoms, 1265 bonds, 175 residues, 5 models selected
> show sel target a
> color sel byhetero
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #6
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #6
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> select /P:445:450:451:458:464:465:470:473-475:477:482:484:488:489:492:496
1014 atoms, 1008 bonds, 102 residues, 6 models selected
> show sel target a
> color sel byhetero
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'C' for virtual key 8 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'c' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00e7' for virtual key 8 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u00c7' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x3' for virtual key 8 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> close
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #1
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #1
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> transparency /N,T,W 20 target s
> select /P:300:310:487:498:513
38 atoms, 33 bonds, 5 residues, 1 model selected
> show sel target a
> color sel byhetero
> log metadata #1
Metadata for 8gkh #1
---
Title | Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex
with ω RNA and target DNA
Citation | Saito, M., Xu, P., Faure, G., Maguire, S., Kannan, S., Altae-Tran,
H., Vo, S., Desimone, A., Macrae, R.K., Zhang, F. (2023). Fanzor is a
eukaryotic programmable RNA-guided endonuclease. Nature. PMID: 37380027. DOI:
10.1038/s41586-023-06356-2
Non-standard residues | MG — magnesium ion
ZN — zinc ion
Gene sources | Methanosarcina mazei
Spizellomyces punctatus
CryoEM Map | EMDB 40184 — open map
Experimental method | Electron microscopy
Resolution | 2.7Å
> log metadata #1
Metadata for 8gkh #1
---
Title | Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex
with ω RNA and target DNA
Citation | Saito, M., Xu, P., Faure, G., Maguire, S., Kannan, S., Altae-Tran,
H., Vo, S., Desimone, A., Macrae, R.K., Zhang, F. (2023). Fanzor is a
eukaryotic programmable RNA-guided endonuclease. Nature. PMID: 37380027. DOI:
10.1038/s41586-023-06356-2
Non-standard residues | MG — magnesium ion
ZN — zinc ion
Gene sources | Methanosarcina mazei
Spizellomyces punctatus
CryoEM Map | EMDB 40184 — open map
Experimental method | Electron microscopy
Resolution | 2.7Å
> select :MG
2 atoms, 2 residues, 1 model selected
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(NoModifier)
Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with
QFlags(ShiftModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ControlModifier)
Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags(AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags(ShiftModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u221a' for virtual key 9 with
QFlags(ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\u25ca' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ControlModifier|AltModifier|MetaModifier)
Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with
QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier)
> open 8gkh
8gkh title:
Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex with ω RNA
and target DNA [more info...]
Chain information for 8gkh #2
---
Chain | Description | UniProt
N | DNA (5'-D(P*CP*GP*GP*TP*AP*CP*CP*CP*GP*GP*GP*CP*AP*TP*A)-3') |
P | Maltodextrin-binding protein (Fragment),OrfB_Zn_ribbon domain-containing
protein | A0A0F8NYV9_METMZ -376--8, A0A0L0H5U9_SPIPD 2-638
T | DNA (35-MER) |
W | RNA (78-MER) |
Non-standard residues in 8gkh #2
---
MG — magnesium ion
ZN — zinc ion
> lighting soft
> graphics silhouettes true width 1
> hide target sacp
> show /P target c
> show /N,T,W target s
> color /W thistle
> color /T red
> color /N dodger blue
> color /P:1-35:275-345 gold
> color /P:36-274 dark gray
> color /P:346-353 white
> color /P:354-546:605-638 medium sea green
> color /P:547-604 hot pink
> transparency /N,T,W 20 target s
> select /P:300:310:487:498:513
76 atoms, 66 bonds, 10 residues, 2 models selected
> show sel target a
> color sel byhetero
> log metadata #2
Metadata for 8gkh #2
---
Title | Structure of the Spizellomyces punctatus Fanzor (SpuFz) in complex
with ω RNA and target DNA
Citation | Saito, M., Xu, P., Faure, G., Maguire, S., Kannan, S., Altae-Tran,
H., Vo, S., Desimone, A., Macrae, R.K., Zhang, F. (2023). Fanzor is a
eukaryotic programmable RNA-guided endonuclease. Nature. PMID: 37380027. DOI:
10.1038/s41586-023-06356-2
Non-standard residues | MG — magnesium ion
ZN — zinc ion
Gene sources | Methanosarcina mazei
Spizellomyces punctatus
CryoEM Map | EMDB 40184 — open map
Experimental method | Electron microscopy
Resolution | 2.7Å
Unsupported scale factor (0.000000) detected on Display0
QPainter::begin: Paint device returned engine == 0, type: 3
===== 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.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,4
Processor Name: Quad-Core Intel Core i5
Processor Speed: 1.4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 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日 2時間 7分
Graphics/Displays:
Intel Iris Plus Graphics 645:
Chipset Model: Intel Iris Plus Graphics 645
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3ea6
Revision ID: 0x0001
Metal Support: Metal 3
Displays:
LG IPS QHD:
Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
UI Looks like: 2560 x 1440 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: 302NTJJEX052
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 7.59
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
| 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 , 2 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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