id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16853	Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0	dmitrii.shiriaev@…	Eric Pettersen	"{{{
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  
  

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> 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

> color #2/B2 blue

> color #2/B3 blue

> color #2/B4 blue

> color #2/B5 blue

> color #2/B6 blue

> color #2/B7 blue

> color #2/B8 blue

> color #2/B9 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/BI blue

> color #2/BJ blue

> color #2/BK blue

> color #2/BL blue

> color #2/BN blue

> color #2/BO blue

> color #2/BP blue

> color #2/BQ blue

> color #2/BR blue

> color #2/BS blue

> 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

> color #3/J3 blue

> color #3/K3 blue

> color #3/L3 blue

> color #3/M3 blue

> color #3/N3 blue

> color #3/O3 blue

> color #3/P3 blue

> color #3/Q3 blue

> color #3/R3 blue

> color #3/S3 blue

> color #3/T3 blue

> color #3/U3 blue

> color #3/V3 blue

> color #3/W3 blue

> color #3/X3 blue

> color #3/Y3 blue

> color #3/Z3 blue

> color #3/03 blue

> color #3/13 blue

> color #3/23 blue

> color #3/33 blue

> color #3/43 blue

> color #3/53 blue

> color #3/63 blue

> color #3/73 blue

> color #3/93 blue

> color #3/a3 blue

> color #3/b3 blue

> color #3/c3 blue

> color #3/d3 blue

> color #3/e3 blue

> color #3/f3 blue

> color #3/g3 blue

> color #3/h3 blue

> color #3/i3 blue

> color #3/j3 blue

> color #3/k3 blue

> color #3/l3 blue

> color #3/m3 blue

> color #3/o3 blue

> color #3/p3 blue

> color #3/q3 blue

> color #3/r3 blue

> color #3/s3 blue

> color #3/t3 blue

> color #3/u3 blue

> color #3/B6 yellow

> color #3/C6 yellow

> color #3/D6 yellow

> color #3/E6 yellow

> color #3/F6 yellow

> color #3/G6 yellow

> color #3/H6 yellow

> color #3/I6 yellow

> color #3/J6 yellow

> color #3/K6 yellow

> color #3/L6 yellow

> color #3/M6 yellow

> color #3/N6 yellow

> color #3/O6 yellow

> color #3/P6 yellow

> color #3/Q6 yellow

> color #3/R6 yellow

> color #3/S6 yellow

> color #3/T6 yellow

> color #3/U6 yellow

> color #3/V6 yellow

> color #3/W6 yellow

> color #3/X6 yellow

> color #3/Y6 yellow

> color #3/Z6 yellow

> color #3/a6 yellow

> color #3/b6 yellow

> color #3/c6 yellow

> color #3/d6 yellow

> color #3/e6 yellow

> color #3/A6 yellow

> color #5/B1 blue

> color #5/B2 blue

> color #5/B3 blue

> color #5/B4 blue

> color #5/B5 blue

> color #5/B6 blue

> color #5/B7 blue

> color #5/B8 blue

> color #5/B9 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/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
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX