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Opened 8 months ago
Closed 8 months ago
#16853 closed defect (duplicate)
Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | 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: Segmentation fault
Thread 0x00007000200c7000 (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 0x000070001f0c4000 (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 0x000070001e0c1000 (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 0x000070001d0be000 (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 0x000070001c0bb000 (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 0x000070001b0b8000 (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 0x000070001a0b5000 (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 0x00007000190b2000 (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 0x00007000180af000 (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 0x00007000170ac000 (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 0x00007000160a9000 (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 0x00007000150a6000 (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 0x00007000140a3000 (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 0x00007000130a0000 (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 0x000070001209d000 (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 0x00007ff849f4dfc0 (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":"2025-02-13 17:05:42.00 +0100","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 14.7.3 (23H417)","roots_installed":0,"name":"ChimeraX","incident_id":"98B59490-AC18-4328-8AB8-C133CBE31A29"}
{
"uptime" : 140000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro16,1",
"coalitionID" : 58473,
"osVersion" : {
"train" : "macOS 14.7.3",
"build" : "23H417",
"releaseType" : "User"
},
"captureTime" : "2025-02-13 17:05:07.6132 +0100",
"codeSigningMonitor" : 0,
"incident" : "98B59490-AC18-4328-8AB8-C133CBE31A29",
"pid" : 66517,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-02-13 16:19:29.5318 +0100",
"procStartAbsTime" : 141056290702524,
"procExitAbsTime" : 143780236168811,
"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":"281472D0-583F-5C6D-AAB7-9E1FDBD890B8","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "69F1B9D9-604E-01D5-03EF-91F38D4674EF",
"lowPowerMode" : 1,
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"wakeTime" : 7,
"bridgeVersion" : {"build":"22P3051","train":"9.3"},
"sleepWakeUUID" : "B68F18D2-EFF7-4D9A-ACA7-BFBE8BEC7716",
"sip" : "enabled",
"vmRegionInfo" : "0x18 is not in any region. Bytes before following region: 4526018536\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dc59000-10dc5a000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"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":66517},
"vmregioninfo" : "0x18 is not in any region. Bytes before following region: 4526018536\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10dc59000-10dc5a000 [ 4K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX",
"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" : [{"queue":"com.apple.main-thread","instructionState":{"instructionStream":{"bytes":[102,231,255,235,7,235,2,235,0,72,137,195,72,131,125,192,0,116,9,72,139,125,192,232,199,36,41,0,72,137,223,232,249,38,41,0,102,15,31,132,0,0,0,0,0,85,72,137,229,65,87,65,86,65,84,83,72,131,236,64,73,137,247,73,137,254,72,199,7,0,0,0,0,72,137,247,232,172,255,223,255,102,46,15,31,132,0,0,0,0,0,102,144,72,137,195,72,139,120,24,72,139,7,255,80,24,72,133,192,117,238,72,137,223,232,6,124,221,255,72,139,123,24,72,139,7,255,80,32,72,133,192,116,32,73,139,62,73,137,6,72,133,255,15,132,204,1,0,0,72,131,196,64,91,65,92,65,94,65,95,93,233,61,36,41,0,72,139,3,72,137,223,255,144,168,0,0,0,131,248,9,117,61,76,137,255,232,254,254,223,255,72],"offset":96}},"frames":[{"imageOffset":32150,"symbol":"__pthread_kill","symbolLocation":10,"imageIndex":143},{"imageOffset":24253,"symbol":"pthread_kill","symbolLocation":262,"imageIndex":144},{"imageOffset":282792,"symbol":"raise","symbolLocation":24,"imageIndex":145},{"imageOffset":16349,"symbol":"_sigtramp","symbolLocation":29,"imageIndex":146},{"imageOffset":0,"imageIndex":147},{"imageOffset":48058,"imageIndex":72},{"imageOffset":87816,"imageIndex":72},{"imageOffset":504101,"symbol":"QCommonStyle::drawControl(QStyle::ControlElement, 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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
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 6zsg 6gaw 7a5g 6vmi 8oin
Summary of feedback from opening 6zsg fetched from pdb
---
warning | Expected gap or connection between 004 /A:7 and MHT /A:8
Summary of feedback from opening 6gaw fetched from pdb
---
notes | Fetching compressed mmCIF 6gaw from
http://files.rcsb.org/download/6gaw.cif
Fetching CCD NA from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/NA/NA.cif
Summary of feedback from opening 7a5g fetched from pdb
---
notes | Fetching compressed mmCIF 7a5g from
http://files.rcsb.org/download/7a5g.cif
Fetching CCD CL from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/CL/CL.cif
Summary of feedback from opening 6vmi fetched from pdb
---
note | Fetching compressed mmCIF 6vmi from
http://files.rcsb.org/download/6vmi.cif
Summary of feedback from opening 8oin fetched from pdb
---
notes | Fetching compressed mmCIF 8oin from
http://files.rcsb.org/download/8oin.cif
Fetching CCD K from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/K/K/K.cif
6zsg title:
Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P-site tRNA
and E-site tRNA [more info...]
Chain information for 6zsg #1
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | Quinupristin |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 |
CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial |
PTCD3_HUMAN 1-689
AA | 12S mitochondrial rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 2-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
XA | 16S mitochondrial rRNA |
XB | mitochondrial tRNAVal |
XD | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
XE | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
XF | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
XH | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
XI | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
XJ | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-190
XK | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
XL | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
XM | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
XN | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
XO | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
XP | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
XQ | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
XR | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
XS | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
XT | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
XU | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
XV | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
XW | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
XX | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
XY | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
XZ | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 8-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-127
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 |
G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
r1 | mRNA |
r2 | A-site tRNA |
r3 | P-site tRNA |
r4 | E-site tRNA |
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
t1 t2 t3 t4 t5 t6 | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN
-60-137
Non-standard residues in 6zsg #1
---
004 — (2S)-amino(phenyl)ethanoic acid (L-Phenylglycine)
DBB — D-α-aminobutyric acid
DOL — 5-(2-diethylamino-
ethanesulfonyl)-21-hydroxy-10-isopropyl-11,19-dimethyl-9,26-dioxa-3,15,28-triaza-
tricyclo[23.2.1.00,255]octacosa-1(27),12,17,19,25(28)-pentaene-2,8,14,23-tetraone
(dalfopristin)
GTP — guanosine-5'-triphosphate
MG — magnesium ion
MHT — (3S)-3-(methylsulfanyl)-1-azabicyclo[2.2.2]octane
MHU — 4-N,N-(dimethylamino)-L-phenylalanine
MHV — 4-oxo-L-pipecolic acid
MHW — 3-hydroxypicolinic acid
P5P — purine riboside-5'-monophosphate
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
6gaw title:
Unique features of mammalian mitochondrial translation initiation revealed by
cryo-EM. This file contains the complete 55S ribosome. [more info...]
Chain information for 6gaw #2
---
Chain | Description | UniProt
AA | 12S ribosomal RNA, mitochondrial |
AB | Mitochondrial ribosomal protein S2 | F1S001_PIG 1-289
AC | Mitochondrial ribosomal protein S24 | A0A287ANU4_PIG 1-167
AE | Mitochondrial ribosomal protein S5 | F1SU66_PIG 1-430
AF | Mitochondrial ribosomal protein S6 | I3LEJ9_PIG 1-124
AG | Mitochondrial ribosomal protein S7 | A0A286ZJ25_PIG 1-242
AI | 28S ribosomal protein S9, mitochondrial | I3LU08_PIG 1-397
AJ | Mitochondrial ribosomal protein S10 | F1RUU2_PIG 1-201
AK | 28S ribosomal protein S11, mitochondrial | A0A286ZJJ6_PIG 1-196
AL | Mitochondrial ribosomal protein S12 | A0A0M3KL52_PIG 1-139
AN | Mitochondrial ribosomal protein S14 | A0A0M3KL53_PIG 1-128
AO | Uncharacterized protein | A0A287BMP0_PIG 1-239
AP | bS16m |
AQ | uS17m | F1RIU0_PIG 1-130
AR | Mitochondrial ribosomal protein S18C | A0A0M3KL54_PIG 1-143
AU | bS21m | A0A286ZNB3_PIG 1-87
AV | P-site fMet-tRNAMet, mitochondrial |
AX | MT-CO3 mRNA, mitochondrial |
AZ | unassigned secondary structure elements |
Aa | Mitochondrial ribosomal protein S22 | A0A287AQT5_PIG 1-382
Ab | 28S ribosomal protein S23, mitochondrial | A0A287AEW3_PIG 1-190
Ac | Mitochondrial ribosomal protein S25 | A0A0M3KL55_PIG 1-173
Ad | Mitochondrial ribosomal protein S26 | A0A287AY01_PIG 1-205
Ae | mS27 |
Af | 28S ribosomal protein S28, mitochondrial | A0A0M3KL56_PIG 1-188
Ag | Death associated protein 3 | I3LS10_PIG 1-397
Ah | mS31 |
Ai | mS33 | F1S8G3_PIG 1-106
Aj | 28S ribosomal protein S34, mitochondrial | F1RG19_PIG 1-218
Ak | 28S ribosomal protein S35, mitochondrial | F1SG95_PIG 1-325
Am | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 |
F1SU49_PIG 1-118
An | Aurora kinase A interacting protein 1 | A0A287B3R8_PIG 1-199
Ao | Pentatricopeptide repeat domain-containing protein 3, mitochondrial |
K7GKS8_PIG 1-692
Ap | 28S ribosomal protein S18b, mitochondrial | RT18B_PIG 1-258
B0 | Mitochondrial ribosomal protein L27 | F1RT79_PIG 1-148
B1 | Mitochondrial ribosomal protein L28 | A0A286ZTW8_PIG 1-256
B2 | Mitochondrial ribosomal protein L47 | F1SGC7_PIG 1-252
B3 | uL30m | F1STE5_PIG 1-161
B4 | 39S ribosomal protein L55, mitochondrial | I3L9J0_PIG 1-126
B5 | bL32m | I3LTC4_PIG 1-188
B6 | bL33m | A0A286ZU68_PIG 1-65
B7 | Mitochondrial ribosomal protein L34 | A0A287A119_PIG 1-95
B8 | Mitochondrial ribosomal protein L35 | F1SVC5_PIG 1-188
B9 | Ribosomal protein | A0A287A731_PIG 1-100
BA | 16S ribosomal RNA, mitochondrial |
BB | tRNA-Phe, mitochondrial |
BC | Translation initiation factor IF-2, mitochondrial | IF2M_HUMAN 78-727
BD | 39S ribosomal protein L2, mitochondrial | F1RRN2_PIG 1-306
BE | ICT1 | A0A140UHW4_PIG 1-348
BF | Mitochondrial ribosomal protein L4 | A0A287B9C4_PIG 1-294
BI | Mitochondrial ribosomal protein L9 | I3LR45_PIG 1-268
BJ | Mitochondrial ribosomal protein L10 | F1RWJ0_PIG 1-262
BK | Mitochondrial ribosomal protein L11 | F1RU54_PIG 1-192
BL CL DL EL FL GL HL | Mitochondrial ribosomal protein L12 | A0A287ARV8_PIG
-35-162 1-198
BN | 39S ribosomal protein L13, mitochondrial | K7GP19_PIG 1-178
BO | uL14m | A0A287BMZ6_PIG 1-145
BP | 39S ribosomal protein L15, mitochondrial | F1RSH0_PIG 1-296
BQ | 39S ribosomal protein L16, mitochondrial | F1RI89_PIG 1-251
BR | 39S ribosomal protein L17, mitochondrial | F1RMQ4_PIG 1-169
BS | Mitochondrial ribosomal protein L18 | A0A286ZNK1_PIG 1-180
BT | Mitochondrial ribosomal protein L19 | I3LNJ0_PIG 1-292
BU | Mitochondrial ribosomal protein L20 | A0A286ZU56_PIG 1-149
BV | Mitochondrial ribosomal protein L21 | F1RY70_PIG 1-209
BW | uL22m | F1RQC9_PIG 1-210
BX | uL23m | A0A286ZZC6_PIG 1-150
BY | 39S ribosomal protein L24, mitochondrial | F1RHJ1_PIG 1-216
Ba | Mitochondrial ribosomal protein L37 | A0A287BIV6_PIG 1-423
Bb | Mitochondrial ribosomal protein L38 | F1RW03_PIG 1-380
Bc | Mitochondrial ribosomal protein L39 | F1SHP6_PIG 1-334
Bd | 39S ribosomal protein L40, mitochondrial isoform 1 | A0A286ZP98_PIG 1-206
Be | Mitochondrial ribosomal protein L41 | A0A287AWS0_PIG 1-135
Bf | mL42 | A0A287BQA1_PIG 1-142
Bg | mL43 | F1S8U4_PIG 1-159
Bh | 39S ribosomal protein L44, mitochondrial | F1SR64_PIG 1-332
Bi | mL45 | I3LGM5_PIG 1-306
Bj | Mitochondrial ribosomal protein L46 | F1SRT0_PIG 1-279
Bk | Mitochondrial ribosomal protein L48 | F1SUS9_PIG 1-212
Bl | 39S ribosomal protein L49, mitochondrial | A0A0R4J8D6_PIG 1-166
Bm | mL50 | I3L9H6_PIG 1-159
Bn | Mitochondrial ribosomal protein L51 | A0A287BE26_PIG 1-128
Bo | 39S ribosomal protein L52, mitochondrial | F1S9B7_PIG 1-124
Bp | mL53 |
Bq | mL54 | I3LN63_PIG 1-138
Bt | Mitochondrial ribosomal protein L57 | A0A287BP93_PIG 1-102
Bu | Peptidyl-tRNA hydrolase ICT1, mitochondrial | A0A286ZJR2_PIG 1-205
Bv | mL64 | A0A286ZXA6_PIG 1-222
Bw | mL65 |
Bx | Mitochondrial ribosomal protein S18A | F1RRH6_PIG 1-196
Bz | unassigned secondary structure elements |
Non-standard residues in 6gaw #2
---
5GP — guanosine-5'-monophosphate
FME — N-formylmethionine
GSP — 5'-guanosine-diphosphate-monothiophosphate
GTP — guanosine-5'-triphosphate
MG — magnesium ion
NA — sodium ion
SPM — spermine
ZN — zinc ion
7a5g title:
Structure of the elongating human mitoribosome bound to mtEF-Tu.GMPPCP and A/T
mt-tRNA [more info...]
Chain information for 7a5g #3
---
Chain | Description | UniProt
03 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
13 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
23 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
24 C | P tRNA |
33 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
43 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
53 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
63 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
73 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
93 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
A3 | 16S rRNA |
A5 | Oxa1L tail |
A6 | 12S rRNA |
B3 | mt-tRNAVal |
B6 | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
C6 | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
D H3 | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
D3 | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
D6 | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
E3 | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
E6 | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
F3 | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
F6 | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
G6 | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
H6 | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
I3 | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
I6 | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
J3 | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192
J6 | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
K3 | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
K6 | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
L3 | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
L6 | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 1-257
M3 | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
M6 | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
N3 | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
N6 | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
O3 | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
O6 | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
P3 | 39S ribosomal protein L18, mitochondrial | RM18_HUMAN 0-179
P6 | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
Q3 | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
Q6 | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
R3 | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
R6 | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
S3 | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
S6 | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
T3 | 39S ribosomal protein L22, mitochondrial | RM22_HUMAN 7-212
T6 | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
U3 | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
U6 | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
V3 | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
V6 | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
W3 | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
W6 | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
X3 | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
X6 | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
Y2 | nascent chain |
Y3 | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
Y6 | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
Z | Elongation factor Tu, mitochondrial | EFTU_HUMAN 1-452
Z3 | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
Z6 | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
a3 | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
a6 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
b3 | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-215
b6 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
c3 | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
c6 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 |
CHCH1_HUMAN 1-118
d3 | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306
d6 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
e3 | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
e6 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial |
PTCD3_HUMAN 1-689
f3 | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-212
g3 | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h3 | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i3 | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
i4 | mRNA |
j | E tRNA |
j3 | 39S ribosomal protein L52, mitochondrial | RM52_HUMAN 1-123
k3 | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l3 | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m3 | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128
n | 50S ribosomal protein L1 | RL1_THET2 0-228
o3 | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p3 | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q3 | Growth arrest and DNA damage-inducible proteins-interacting protein 1 |
G45IP_HUMAN 1-222
r3 | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
s3 t3 | 39S ribosomal protein S30, mitochondrial,39S ribosomal protein S30,
mitochondrial,mL65 | RT30_HUMAN -438-0 1-439
u3 | RNA (5'-R(P*CP*A)-3') |
Non-standard residues in 7a5g #3
---
CL — chloride ion
GCP — phosphomethylphosphonic acid guanylate ester
GDP — guanosine-5'-diphosphate
MG — magnesium ion
MLI — malonate ion
NA — sodium ion
SO4 — sulfate ion
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
ZN — zinc ion
6vmi title:
Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII) [more
info...]
Chain information for 6vmi #4
---
Chain | Description | UniProt
0 | 39S ribosomal protein L32, mitochondrial | RM32_HUMAN 1-188
1 | 39S ribosomal protein L33, mitochondrial | RM33_HUMAN 1-65
2 | 39S ribosomal protein L34, mitochondrial | RM34_HUMAN 1-92
3 | 39S ribosomal protein L35, mitochondrial | RM35_HUMAN 1-188
4 | 39S ribosomal protein L36, mitochondrial | RM36_HUMAN 1-103
5 | 39S ribosomal protein L37, mitochondrial | RM37_HUMAN 1-423
6 | 39S ribosomal protein L38, mitochondrial | RM38_HUMAN 1-380
7 | 39S ribosomal protein L39, mitochondrial | RM39_HUMAN 1-338
8 | 39S ribosomal protein L40, mitochondrial | RM40_HUMAN 1-206
9 | 39S ribosomal protein L41, mitochondrial | RM41_HUMAN 1-137
A | 16s rRNA |
A0 | 28S ribosomal protein S34, mitochondrial | RT34_HUMAN 1-218
A1 | 28S ribosomal protein S35, mitochondrial | RT35_HUMAN 1-323
A2 | Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 |
CHCH1_HUMAN 1-118
A3 | Aurora kinase A-interacting protein | AKIP_HUMAN 1-199
A4 | Pentatricopeptide repeat domain-containing protein 3, mitochondrial |
PTCD3_HUMAN 1-689
A5 | mRNA |
A6 A7 | P-site and E-site tRNA |
AA | 12s rRNA |
AB | 28S ribosomal protein S2, mitochondrial | RT02_HUMAN 1-296
AC | 28S ribosomal protein S24, mitochondrial | RT24_HUMAN 1-167
AD | 28S ribosomal protein S5, mitochondrial | RT05_HUMAN 1-430
AE | 28S ribosomal protein S6, mitochondrial | RT06_HUMAN 1-125
AF | 28S ribosomal protein S7, mitochondrial | RT07_HUMAN 1-242
AG | 28S ribosomal protein S9, mitochondrial | RT09_HUMAN 1-396
AH | 28S ribosomal protein S10, mitochondrial | RT10_HUMAN 1-201
AI | 28S ribosomal protein S11, mitochondrial | RT11_HUMAN 1-194
AJ | 28S ribosomal protein S12, mitochondrial | RT12_HUMAN 1-138
AK | 28S ribosomal protein S14, mitochondrial | RT14_HUMAN 1-128
AL | 28S ribosomal protein S15, mitochondrial | RT15_HUMAN 0-256
AM | 28S ribosomal protein S16, mitochondrial | RT16_HUMAN 1-137
AN | 28S ribosomal protein S17, mitochondrial | RT17_HUMAN 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_HUMAN 1-258
AP | 28S ribosomal protein S18c, mitochondrial | RT18C_HUMAN 1-142
AQ | 28S ribosomal protein S21, mitochondrial | RT21_HUMAN 1-87
AR | 28S ribosomal protein S22, mitochondrial | RT22_HUMAN 1-360
AS | 28S ribosomal protein S23, mitochondrial | RT23_HUMAN 1-190
AT | 28S ribosomal protein S25, mitochondrial | RT25_HUMAN 1-173
AU | 28S ribosomal protein S26, mitochondrial | RT26_HUMAN 1-205
AV | 28S ribosomal protein S27, mitochondrial | RT27_HUMAN 1-414
AW | 28S ribosomal protein S28, mitochondrial | RT28_HUMAN 1-187
AX | 28S ribosomal protein S29, mitochondrial | RT29_HUMAN 1-398
AY | 28S ribosomal protein S31, mitochondrial | RT31_HUMAN 1-395
AZ | 28S ribosomal protein S33, mitochondrial | RT33_HUMAN 1-106
B | tRNAval |
D | 39S ribosomal protein L2, mitochondrial | RM02_HUMAN 1-305
E | 39S ribosomal protein L3, mitochondrial | RM03_HUMAN 1-348
F | 39S ribosomal protein L4, mitochondrial | RM04_HUMAN 1-311
H | 39S ribosomal protein L9, mitochondrial | RM09_HUMAN 1-267
I | 39S ribosomal protein L10, mitochondrial | RM10_HUMAN 1-261
J | 39S ribosomal protein L11, mitochondrial | RM11_HUMAN 1-192
K | 39S ribosomal protein L13, mitochondrial | RM13_HUMAN 1-178
L | 39S ribosomal protein L14, mitochondrial | RM14_HUMAN 1-145
M | 39S ribosomal protein L15, mitochondrial | RM15_HUMAN 1-296
N | 39S ribosomal protein L16, mitochondrial | RM16_HUMAN 1-251
O | 39S ribosomal protein L17, mitochondrial | RM17_HUMAN 1-175
P | Mitochondrial ribosomal protein L18, isoform CRA_b | A8K9D2_HUMAN 2-180
Q | 39S ribosomal protein L19, mitochondrial | RM19_HUMAN 1-292
R | 39S ribosomal protein L20, mitochondrial | RM20_HUMAN 1-149
S | 39S ribosomal protein L21, mitochondrial | RM21_HUMAN 1-205
T | 39S ribosomal protein L22, mitochondrial | E7ESL0_HUMAN 1-212
TA TB TC | 39S ribosomal protein L12, mitochondrial | RM12_HUMAN 1-198
U | 39S ribosomal protein L23, mitochondrial | RM23_HUMAN 1-153
V | 39S ribosomal protein L24, mitochondrial | RM24_HUMAN 1-216
W | 39S ribosomal protein L27, mitochondrial | RM27_HUMAN 1-148
X | 39S ribosomal protein L28, mitochondrial | RM28_HUMAN 1-256
Y | 39S ribosomal protein L47, mitochondrial | RM47_HUMAN 1-250
Z | 39S ribosomal protein L30, mitochondrial | RM30_HUMAN 1-161
a | 39S ribosomal protein L42, mitochondrial | RM42_HUMAN 1-142
b | 39S ribosomal protein L43, mitochondrial | RM43_HUMAN 1-155
c | 39S ribosomal protein L44, mitochondrial | RM44_HUMAN 1-332
d | 39S ribosomal protein L45, mitochondrial | RM45_HUMAN 1-306
e | 39S ribosomal protein L46, mitochondrial | RM46_HUMAN 1-279
f | 39S ribosomal protein L48, mitochondrial | RM48_HUMAN 1-194
g | 39S ribosomal protein L49, mitochondrial | RM49_HUMAN 1-166
h | 39S ribosomal protein L50, mitochondrial | RM50_HUMAN 1-158
i | 39S ribosomal protein L51, mitochondrial | RM51_HUMAN 1-128
j | cDNA FLJ76418, highly similar to Homo sapiens mitochondrial ribosomal
protein L52 (MRPL52), transcript variant 1, mRNA | A8K7J6_HUMAN 1-123
k | 39S ribosomal protein L53, mitochondrial | RM53_HUMAN 1-112
l | 39S ribosomal protein L54, mitochondrial | RM54_HUMAN 1-138
m | 39S ribosomal protein L55, mitochondrial | RM55_HUMAN 1-128
o | Ribosomal protein 63, mitochondrial | RT63_HUMAN 1-102
p | Peptidyl-tRNA hydrolase ICT1, mitochondrial | ICT1_HUMAN 1-206
q | Growth arrest and DNA damage-inducible proteins-interacting protein 1 |
G45IP_HUMAN 1-222
r | 39S ribosomal protein S18a, mitochondrial | RT18A_HUMAN 1-196
s | 39S ribosomal protein S30, mitochondrial | RT30_HUMAN 1-439
u | P-site finger |
v | Elongation factor G, mitochondrial | EFGM_HUMAN 1-751
Non-standard residues in 6vmi #4
---
GCP — phosphomethylphosphonic acid guanylate ester
GDP — guanosine-5'-diphosphate
MG — magnesium ion
P5P — purine riboside-5'-monophosphate
Y5P — 1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine (pyrimidine
riboside-5'-monophosphate)
ZN — zinc ion
8oin title:
55S mammalian mitochondrial ribosome with mtRF1 and P-site tRNA [more info...]
Chain information for 8oin #5
---
Chain | Description | UniProt
AA | 12S rRNA |
AB | 28S ribosomal protein S35, mitochondrial isoform 1 | F1SG95_PIG -40-325
AC | Mitochondrial ribosomal protein S24 | A0A287ANU4_PIG 1-167
AD | Small ribosomal subunit protein mS38 | A0A8D1P8R7_PIG 1-199
AE | Mitoribosomal protein bs6m, mrps6 | A0A5K1V0G5_PIG 1-124
AF | Mitochondrial ribosomal protein S7 | A0A286ZJ25_PIG 1-242
AG | P-site Met-tRNA(fMet) |
AH | Mitochondrial ribosomal protein S10 | F1RUU2_PIG 2-201
AI | mRNA |
AJ | Mitochondrial ribosomal protein S12 | A0A0M3KL52_PIG 1-139
AK | Mitochondrial ribosomal protein S14 | A0A0M3KL53_PIG 1-128
AL | 28S ribosomal protein S15, mitochondrial | A0A287AKS1_PIG -19-239
AM | 28S ribosomal protein S16, mitochondrial | A0A480JTD7_PIG 1-135
AN | 28S ribosomal protein S17, mitochondrial | A0A8D1IXU1_PIG 1-130
AO | 28S ribosomal protein S18b, mitochondrial | RT18B_PIG 1-258
AP | Mitochondrial ribosomal protein S18C | A0A0M3KL54_PIG 1-143
AQ | 28S ribosomal protein S21, mitochondrial | A0A286ZNB3_PIG 1-87
AR | Mitochondrial ribosomal protein S22 | A0A287AQT5_PIG 1-382
AS | mS23 | A0A287AEW3_PIG 1-190
AT | Mitochondrial ribosomal protein S25 | A0A0M3KL55_PIG 1-173
AU | Mitochondrial ribosomal protein S26 | A0A287AY01_PIG 1-205
AV | Mitochondrial ribosomal protein S27 | A0A5G2R1I0_PIG 61-455
AW | Mitoribosomal protein ms28, mrps28 | A0A0M3KL56_PIG 1-188
AX | Small ribosomal subunit protein mS29 | A0A8D1XNL0_PIG -12-397
AY | 28S ribosomal protein S31, mitochondrial | F1RME2_PIG 7-387
AZ | Mitochondrial ribosomal protein S33 | F1S8G3_PIG -41-106
Aa | Peptide chain release factor 1, mitochondrial | RF1M_HUMAN 1-445
Ab | Mitochondrial ribosomal protein S2 | F1S001_PIG 1-289
Ac | Coiled-coil-helix-coiled-coil-helix domain containing 1 | F1SU49_PIG
1-118
Ad | 28S ribosomal protein S5, mitochondrial isoform X2 | F1SU66_PIG 1-430
Ae | mS39 | K7GKS8_PIG 1-692
Ag | uS9m | I3LU08_PIG 1-397
Ai | Mitochondrial ribosomal protein S11 | A0A286ZJJ6_PIG 1-196
Aj | Mitochondrial ribosomal protein S34 | A0A287AVS9_PIG -286-218
B1 B2 B3 B4 B5 B6 | Mitochondrial ribosomal protein L12 | A0A8D0VGD9_PIG
-35-162 1-198
B7 | E-site tRNA |
B8 | 16S rRNA |
B9 | CP Phe-tRNA |
BA | Large ribosomal subunit protein uL22m | A0A4X1TXR4_PIG 1-210
BB | 39S ribosomal protein L23, mitochondrial | A0A480JJI1_PIG 1-150
BC | uL24m | F1RHJ1_PIG 1-216
BD | 39S ribosomal protein L27, mitochondrial | A0A4X1U0F6_PIG 1-148
BE | Mitochondrial ribosomal protein L28 | A0A286ZTW8_PIG 1-256
BF | Mitochondrial ribosomal protein L47 | F1SGC7_PIG 3-252
BG | Large ribosomal subunit protein uL30m | A0A8D0VJF4_PIG 1-161
BH | Mitochondrial ribosomal protein L32 | I3LTC4_PIG -18-188
BI | Large ribosomal subunit protein bL33m | A0A4X1TLP9_PIG 1-65
BJ | Large ribosomal subunit protein bL34m | A0A8D1JE64_PIG 1-95
BK | 39S ribosomal protein L35, mitochondrial | A0A5G2QZK0_PIG 1-188
BL | Mitochondrial ribosomal protein L2 | A0A287A143_PIG 1-306
BM | ICT1 | A0A140UHW4_PIG -50-348
BN | Mitochondrial ribosomal protein L4 | A0A287B9C4_PIG 1-294
BO | Mitochondrial ribosomal protein L9 | I3LR45_PIG 1-268
BP | Mitochondrial ribosomal protein L10 | F1RWJ0_PIG 6-262
BQ | Mitochondrial ribosomal protein L11 | F1RU54_PIG 1-192
BR | 39S ribosomal protein L13, mitochondrial | K7GP19_PIG -18-178
BS | Mitochondrial ribosomal protein L14 | A0A287BMZ6_PIG -179-145
BT | 39S ribosomal protein L15, mitochondrial | A0A5G2RG26_PIG 1-296
BU | uL16m | F1RI89_PIG 1-251
BV | bL17m | F1RMQ4_PIG 1-169
BW | Mitochondrial ribosomal protein L18 | A0A4X1VX01_PIG -7-180
BX | 39S ribosomal protein L19, mitochondrial | I3LNJ0_PIG -10-292
BY | Mitochondrial ribosomal protein L20 | A0A286ZU56_PIG 1-149
BZ | Mitochondrial ribosomal protein L21 | F1RY70_PIG 1-209
Ba | 39S ribosomal protein L52, mitochondrial | F1S9B7_PIG -35-124
Bb | Mitochondrial ribosomal protein L53 | A0A8D0LKT0_PIG 1-112
Bc | mL54 | I3LN63_PIG 1-138
Bd | Mitochondrial ribosomal protein L55 | A0A4X1ULI6_PIG 1-126
Be | Mitochondrial ribosomal protein L57 | A0A287BP93_PIG 1-102
Bf | mL62 (ICT1) | A0A286ZJR2_PIG 1-205
Bg | mL64 | A0A286ZXA6_PIG 1-222
Bh | Mitochondrial ribosomal protein S18A | F1RRH6_PIG 1-196
Bi | 39S ribosomal protein S30, mitochondrial | A0A480QIM3_PIG 1-433
Bj | 39S ribosomal protein L1, mitochondrial | A0A287AF82_PIG 22-325
Bl | Ribosomal protein | A0A287A731_PIG 1-100
Bm | Mitochondrial ribosomal protein L37 | A0A287BIV6_PIG 1-423
Bn | Mitochondrial ribosomal protein L38 | F1RW03_PIG 1-380
Bo | Mitochondrial ribosomal protein L39 | F1SHP6_PIG 1-334
Bp | Mitochondrial ribosomal protein L40 | A0A286ZP98_PIG 45-206
Bq | 39S ribosomal protein L41, mitochondrial | A0A8D1BPA5_PIG 1-135
Br | mL42 | A0A287BQA1_PIG 1-142
Bs | Large ribosomal subunit protein mL43 | F1S8U4_PIG 2-159
Bt | mL44 | F1SR64_PIG 1-332
Bu | Mitochondrial ribosomal protein L45 | I3LGM5_PIG 1-306
Bv | Mitochondrial ribosomal protein L46 | F1SRT0_PIG 1-279
Bw | 39S ribosomal protein L48, mitochondrial | A0A480J9Z6_PIG -56-212
Bx | Mrpl34 | A0A0R4J8D6_PIG 1-166
By | Mitochondrial ribosomal protein L50 | I3L9H6_PIG -38-159
Bz | Large ribosomal subunit protein mL51 | A0A8D1VKN8_PIG 1-128
Non-standard residues in 8oin #5
---
1MA — 6-hydro-1-methyladenosine-5'-monophosphate
5F0 — (3~{S})-3-azanyl-4-methoxy-4-oxidanylidene-butanoic acid (1-methyl
isoaspartic acid)
5MC — 5-methylcytidine-5'-monophosphate
5MU — 5-methyluridine 5'-monophosphate
ACE — acetyl group
ATP — adenosine-5'-triphosphate
AYA — N-acetylalanine
B8T — 4-methyl, cytidine-5'-monophosphate
FES — FE2/S2 (inorganic) cluster
FME — N-formylmethionine
GDP — guanosine-5'-diphosphate
K — potassium ion
MA6 — 6N-dimethyladenosine-5'-monophoshate
MG — magnesium ion
MIA — 2-methylthio-N6-isopentenyl-adenosine-5'-monophosphate
OMG — O2'-methylguanosine-5'-monophosphate
OMU — O2'-methyluridine 5'-monophosphate
PHE — phenylalanine
SAC — N-acetyl-serine
SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34))
SPM — spermine
ZN — zinc ion
> hide all atoms
> show all cartoons
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
> color #1-5 color grey
> show #!2 models
> align #2/AJ toAtoms #1/AJ matchNumbering true
Pairing dropped 440 atoms and 1010 reference atoms
RMSD between 715 atom pairs is 23.609 angstroms
> align #2/AJ toAtoms #1/AJ matchNumbering true
Pairing dropped 440 atoms and 1010 reference atoms
RMSD between 715 atom pairs is 23.609 angstroms
> hide #!1 models
> hide #!2 models
> show #!1 models
> show #!2 models
> select #1,2/AJ
2880 atoms, 2922 bonds, 248 residues, 2 models selected
> hide #!2 models
> show #!2 models
> hide #!1 models
> align #2/AJ toAtoms #1/AL matchNumbering true
Pairing dropped 136 atoms and 1835 reference atoms
RMSD between 1019 atom pairs is 22.011 angstroms
> show #!1 models
> align #2/AL toAtoms #1/AJ matchNumbering true
Pairing dropped 9 atoms and 894 reference atoms
RMSD between 831 atom pairs is 2.753 angstroms
> select add #1
316503 atoms, 325809 bonds, 2393 pseudobonds, 17112 residues, 5 models
selected
> select add #2
493720 atoms, 512199 bonds, 4943 pseudobonds, 35025 residues, 8 models
selected
> select subtract #1
178372 atoms, 187571 bonds, 2550 pseudobonds, 18053 residues, 4 models
selected
> select subtract #2
Nothing selected
> align #2/AL toAtoms #1/AJ matchNumbering true
Pairing dropped 9 atoms and 894 reference atoms
RMSD between 831 atom pairs is 2.753 angstroms
> align #3/J6 toAtoms #1/AJ matchNumbering true
Pairing dropped 0 atoms and 887 reference atoms
RMSD between 838 atom pairs is 2.484 angstroms
> align #4/AJ toAtoms #1/AJ matchNumbering true
Pairing dropped 0 atoms and 887 reference atoms
RMSD between 838 atom pairs is 2.540 angstroms
> align #5/AJ toAtoms #1/AJ matchNumbering true
Pairing dropped 10 atoms and 894 reference atoms
RMSD between 831 atom pairs is 2.725 angstroms
> show #!5 models
> hide #!5 models
> show #!4 models
> show #!5 models
> show #!3 models
> hide #!3 models
> hide #!2 models
> hide #!5 models
Drag select of 251 residues
> select clear
> runcsript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
Unknown command: runcsript
/Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
lifecycle/try.py
> runscript
Missing or invalid "scriptFile" argument: Expected a file name
> runscript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
['0' '1' '2' '3' '4' '5' '6' '7' '8' '9' 'XA' 'A0' 'A1' 'A2' 'A3' 'A4'
'AA' 'AB' 'AC' 'AD' 'AE' 'AF' 'AG' 'AH' 'AI' 'AJ' 'AK' 'AL' 'AM' 'AN'
'AO' 'AP' 'AQ' 'AR' 'AS' 'AT' 'AU' 'AV' 'AW' 'AX' 'AY' 'AZ' 'XB' 'XD'
'XE' 'XF' 'XH' 'XI' 'XJ' 'XK' 'XL' 'XM' 'XN' 'XO' 'XP' 'XQ' 'XR' 'XS'
'XT' 'XU' 'XV' 'XW' 'XX' 'XY' 'XZ' 'a' 'b' 'c' 'd' 'e' 'f' 'g' 'h' 'i'
'j' 'k' 'l' 'm' 'o' 'p' 'q' 'r' 'r1' 'r2' 'r3' 'r4' 's' 't1' 't2' 't3'
't4' 't5' 't6' 'A']
> runscript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
> color #1/A0 yellow
> color #1/A1 yellow
> color #1/A2 yellow
> color #1/A3 yellow
> color #1/A4 yellow
> color #1/AA yellow
> color #1/AB yellow
> color #1/AC yellow
> color #1/AD yellow
> color #1/AE yellow
> color #1/AF yellow
> color #1/AG yellow
> color #1/AH yellow
> color #1/AI yellow
> color #1/AJ yellow
> color #1/AK yellow
> color #1/AL yellow
> color #1/AM yellow
> color #1/AN yellow
> color #1/AO yellow
> color #1/AP yellow
> color #1/AQ yellow
> color #1/AR yellow
> color #1/AS yellow
> color #1/AT yellow
> color #1/AU yellow
> color #1/AV yellow
> color #1/AW yellow
> color #1/AX yellow
> color #1/AY yellow
> color #1/AZ yellow
> color #1/A yellow
> runscript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
Traceback (most recent call last):
File
"/Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
lifecycle/try.py", line 18, in
print(n.name)
NameError: name 'n' is not defined
Error opening python file
/Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
lifecycle/try.py
> runscript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
6zsg
Drag select of 8 residues
> select clear
> show #!2 models
> show #!3 models
> show #!5 models
> runscript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
Traceback (most recent call last):
File
"/Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
lifecycle/try.py", line 23, in
chain_ids = m.chains.chain_ids
AttributeError: 'list' object has no attribute 'chains'
Error opening python file
/Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
lifecycle/try.py
> runscript
> /Users/dmitrii.shiriaev/Code/lab/chimerax_scripting/noa1_figures/ribosome-
> lifecycle/try.py
> color #1/XA blue
> color #1/A0 yellow
> color #1/A1 yellow
> color #1/A2 yellow
> color #1/A3 yellow
> color #1/A4 yellow
> color #1/AA yellow
> color #1/AB yellow
> color #1/AC yellow
> color #1/AD yellow
> color #1/AE yellow
> color #1/AF yellow
> color #1/AG yellow
> color #1/AH yellow
> color #1/AI yellow
> color #1/AJ yellow
> color #1/AK yellow
> color #1/AL yellow
> color #1/AM yellow
> color #1/AN yellow
> color #1/AO yellow
> color #1/AP yellow
> color #1/AQ yellow
> color #1/AR yellow
> color #1/AS yellow
> color #1/AT yellow
> color #1/AU yellow
> color #1/AV yellow
> color #1/AW yellow
> color #1/AX yellow
> color #1/AY yellow
> color #1/AZ yellow
> color #1/XB blue
> color #1/XD blue
> color #1/XE blue
> color #1/XF blue
> color #1/XH blue
> color #1/XI blue
> color #1/XJ blue
> color #1/XK blue
> color #1/XL blue
> color #1/XM blue
> color #1/XN blue
> color #1/XO blue
> color #1/XP blue
> color #1/XQ blue
> color #1/XR blue
> color #1/XS blue
> color #1/XT blue
> color #1/XU blue
> color #1/XV blue
> color #1/XW blue
> color #1/XX blue
> color #1/XY blue
> color #1/XZ blue
> color #1/A yellow
> color #2/B0 blue
> color #2/B1 blue
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> color #2/BT blue
> color #2/BU blue
> color #2/BV blue
> color #2/BW blue
> color #2/BX blue
> color #2/BY blue
> color #2/Ba blue
> color #2/Bb blue
> color #2/Bc blue
> color #2/Bd blue
> color #2/Be blue
> color #2/Bf blue
> color #2/Bg blue
> color #2/Bh blue
> color #2/Bi blue
> color #2/Bj blue
> color #2/Bk blue
> color #2/Bl blue
> color #2/Bm blue
> color #2/Bn blue
> color #2/Bo blue
> color #2/Bp blue
> color #2/Bq blue
> color #2/Bt blue
> color #2/Bu blue
> color #2/Bv blue
> color #2/Bw blue
> color #2/Bx blue
> color #2/Bz blue
> color #2/AA yellow
> color #2/AB yellow
> color #2/AC yellow
> color #2/AE yellow
> color #2/AF yellow
> color #2/AG yellow
> color #2/AI yellow
> color #2/AJ yellow
> color #2/AK yellow
> color #2/AL yellow
> color #2/AN yellow
> color #2/AO yellow
> color #2/AP yellow
> color #2/AQ yellow
> color #2/AR yellow
> color #2/AU yellow
> color #2/AV yellow
> color #2/AX yellow
> color #2/AZ yellow
> color #2/Aa yellow
> color #2/Ab yellow
> color #2/Ac yellow
> color #2/Ad yellow
> color #2/Ae yellow
> color #2/Af yellow
> color #2/Ag yellow
> color #2/Ah yellow
> color #2/Ai yellow
> color #2/Aj yellow
> color #2/Ak yellow
> color #2/Am yellow
> color #2/An yellow
> color #2/Ao yellow
> color #2/Ap yellow
> color #3/A3 blue
> color #3/B3 blue
> color #3/D3 blue
> color #3/E3 blue
> color #3/F3 blue
> color #3/H3 blue
> color #3/I3 blue
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> color #3/03 blue
> color #3/13 blue
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> color #3/33 blue
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> color #3/53 blue
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> color #3/B6 yellow
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> color #5/B1 blue
> color #5/B2 blue
> color #5/B3 blue
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> color #5/B5 blue
> color #5/B6 blue
> color #5/B7 blue
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> color #5/BA blue
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> color #5/BG blue
> color #5/BH blue
> color #5/BI blue
> color #5/BJ blue
> color #5/BK blue
> color #5/BL blue
> color #5/BM blue
> color #5/BN blue
> color #5/BO blue
> color #5/BP blue
> color #5/BQ blue
> color #5/BR blue
> color #5/BS blue
> color #5/BT blue
> color #5/BU blue
> color #5/BV blue
> color #5/BW blue
> color #5/BX blue
> color #5/BY blue
> color #5/BZ blue
> color #5/Ba blue
> color #5/Bb blue
> color #5/Bc blue
> color #5/Bd blue
> color #5/Be blue
> color #5/Bf blue
> color #5/Bg blue
> color #5/Bh blue
> color #5/Bi blue
> color #5/Bj blue
> color #5/Bl blue
> color #5/Bm blue
> color #5/Bn blue
> color #5/Bo blue
> color #5/Bp blue
> color #5/Bq blue
> color #5/Br blue
> color #5/Bs blue
> color #5/Bt blue
> color #5/Bu blue
> color #5/Bv blue
> color #5/Bw blue
> color #5/Bx blue
> color #5/By blue
> color #5/Bz blue
> color #5/AA yellow
> color #5/AB yellow
> color #5/AC yellow
> color #5/AD yellow
> color #5/AE yellow
> color #5/AF yellow
> color #5/AG yellow
> color #5/AH yellow
> color #5/AI yellow
> color #5/AJ yellow
> color #5/AK yellow
> color #5/AL yellow
> color #5/AM yellow
> color #5/AN yellow
> color #5/AO yellow
> color #5/AP yellow
> color #5/AQ yellow
> color #5/AR yellow
> color #5/AS yellow
> color #5/AT yellow
> color #5/AU yellow
> color #5/AV yellow
> color #5/AW yellow
> color #5/AX yellow
> color #5/AY yellow
> color #5/AZ yellow
> color #5/Aa yellow
> color #5/Ab yellow
> color #5/Ac yellow
> color #5/Ad yellow
> color #5/Ae yellow
> color #5/Ag yellow
> color #5/Ai yellow
> color #5/Aj yellow
> hide #!2 models
> hide #!3 models
> hide #!4 models
> hide #!5 models
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 ATI-5.5.17
OpenGL renderer: AMD Radeon Pro 5300M OpenGL Engine
OpenGL vendor: ATI Technologies 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: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2,6 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 64 GB
System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13051.0.0,0)
OS Loader Version: 580.140.1~51
Software:
System Software Overview:
System Version: macOS 14.7.3 (23H417)
Kernel Version: Darwin 23.6.0
Time since boot: 5 days, 12 hours, 42 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-019
Option ROM Version: 113-D32207P1-019
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: No
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-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 , 8 months ago
| 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 , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Dmitrii,
--Eric