Opened 2 years ago

Last modified 2 years ago

#10224 closed defect

Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 — at Version 1

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-13.5.2-arm64-arm-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 0x00000002abedf000 (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 0x00000002aaed3000 (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 0x00000002a9ec7000 (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 0x00000002a8ebb000 (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 0x00000002a7eaf000 (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 0x00000002a6ea3000 (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 0x00000002a5e97000 (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 0x00000002a4e8b000 (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 0x00000002a3e7f000 (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 0x00000002a2e73000 (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 0x00000002a1e67000 (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 0x00000002a0e5b000 (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 0x000000029fe4f000 (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 0x0000000294013000 (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 0x0000000293007000 (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 0x00000001dbfc6080 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2023-11-24 18:07:47.00 +0000","app_version":"1.6.1","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.6.1.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5.2 (22G91)","roots_installed":0,"name":"ChimeraX","incident_id":"A684FB98-40D7-4903-8129-E2AE15A53AFF"}
{
  "uptime" : 100000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 503,
  "deployVersion" : 210,
  "modelCode" : "Mac14,9",
  "coalitionID" : 1900,
  "osVersion" : {
    "train" : "macOS 13.5.2",
    "build" : "22G91",
    "releaseType" : "User"
  },
  "captureTime" : "2023-11-24 18:07:45.7233 +0000",
  "incident" : "A684FB98-40D7-4903-8129-E2AE15A53AFF",
  "pid" : 53252,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2023-11-24 11:48:40.9858 +0000",
  "procStartAbsTime" : 2064626040653,
  "procExitAbsTime" : 2430710937210,
  "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":"F403C663-ED3D-5EBD-90E3-1907538C7ACC","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "BF2B3580-A1C4-5A90-B68E-2D28F156E60D",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 0,
  "sleepWakeUUID" : "E6ED89B5-1DF0-42AF-B078-86B7746AD977",
  "sip" : "enabled",
  "vmRegionInfo" : "0x18 is not in any region.  Bytes before following region: 105555129532392\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600078000000-600080000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "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":53252},
  "vmregioninfo" : "0x18 is not in any region.  Bytes before following region: 105555129532392\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      MALLOC_NANO (reserved)   600078000000-600080000000 [128.0M] rw-\/rwx SM=NUL  ...(unallocated)",
  "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" : [{"triggered":true,"id":1579077,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6458637741},{"value":5369363480},{"value":12979183233058688588},{"value":0},{"value":6124892200},{"value":15206481622518462668},{"value":15206481615414597708},{"value":78},{"value":0},{"value":49},{"value":16},{"value":14027849728},{"value":16},{"value":328},{"value":8064512928},{"value":0},{"value":11},{"value":7985717376,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":7985717600,"symbolLocation":224,"symbol":"_main_thread"},{"value":4813724592},{"value":1},{"value":32769},{"value":32768},{"value":7985723808,"symbolLocation":0,"symbol":"_NSConcreteStackBlock"},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6458457128},"cpsr":{"value":1073745920},"fp":{"value":5369363280},"sp":{"value":5369363248},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6458230628,"matchesCrashFrame":1},"far":{"value":10974343744}},"name":"CrBrowserMain","queue":"com.apple.main-thread","frames":[{"imageOffset":38756,"symbol":"__pthread_kill","symbolLocation":8,"imageIndex":154},{"imageOffset":27688,"symbol":"pthread_kill","symbolLocation":288,"imageIndex":155},{"imageOffset":259180,"symbol":"raise","symbolLocation":32,"imageIndex":156},{"imageOffset":14884,"symbol":"_sigtramp","symbolLocation":56,"imageIndex":157},{"imageOffset":3459388,"symbol":"QMacCGContext::QMacCGContext(QPainter*)","symbolLocation":40,"imageIndex":48},{"imageOffset":43052,"imageIndex":69},{"imageOffset":73708,"imageIndex":69},{"imageOffset":464432,"symbol":"QCommonStyle::drawControl(QStyle::ControlElement, QStyleOption const*, QPainter*, QWidget const*) 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[deleted to fit within ticket limits]

> show #!7 models

> hide #9 models

> select #7/D

1135 atoms, 1171 bonds, 146 residues, 1 model selected  

> color sel #ff2600ff

> select clear

> select #7/N

605 atoms, 610 bonds, 77 residues, 1 model selected  

> color sel cyan

> select clear

> volume #17 level 0.1444

> volume #17 level 0.3449

> save "/Users/ccrowe/OneDrive - University of Dundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_24_chimeraxsession.cxs" includeMaps true

> open 8pc2

Summary of feedback from opening 8pc2 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /C:16  
Atom H1 is not in the residue template for MET /D:1  
Atom H1 is not in the residue template for MET /E:16  
Atom H1 is not in the residue template for MET /F:1  
note | Fetching compressed mmCIF 8pc2 from
http://files.rcsb.org/download/8pc2.cif  
  
8pc2 title:  
SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC [more info...]  
  
Chain information for 8pc2 #18  
---  
Chain | Description | UniProt  
A B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
C E | Elongin-C | ELOC_HUMAN 17-112  
D F | Elongin-B | ELOB_HUMAN 1-104  
G H | Peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 16-140  
  
Non-standard residues in 8pc2 #18  
---  
XZW —
[(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-
butanoyl]-4-oxidanyl-
pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl]
(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate  
  
8pc2 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select add #18

14339 atoms, 14505 bonds, 2 pseudobonds, 934 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.28252,0.45894,0.84235,-27.049,-0.48448,0.82616,-0.28763,-24.16,-0.82792,-0.32684,0.45576,-41.649

> view matrix models
> #18,-0.79648,0.26486,0.54357,-78.503,-0.3288,0.56473,-0.75695,-20.263,-0.50745,-0.78162,-0.36271,-32.611

> view matrix models
> #18,-0.99423,0.013299,0.10643,-90.565,-0.084286,0.51682,-0.85194,-9.7222,-0.066335,-0.85599,-0.51272,-13.448

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.99423,0.013299,0.10643,135.52,-0.084286,0.51682,-0.85194,117.45,-0.066335,-0.85599,-0.51272,202.3

> view matrix models
> #18,-0.99423,0.013299,0.10643,138.57,-0.084286,0.51682,-0.85194,118.64,-0.066335,-0.85599,-0.51272,204.28

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.99423,0.013299,0.10643,127.01,-0.084286,0.51682,-0.85194,153.95,-0.066335,-0.85599,-0.51272,200.24

> ui mousemode right "rotate selected models"

> view matrix models
> #18,0.28745,0.93692,-0.19889,163.2,0.33926,-0.29379,-0.89364,188.3,-0.8957,0.1894,-0.40231,143.86

> select #18/B

2587 atoms, 2621 bonds, 157 residues, 1 model selected  

> delete sel

> select #18/H

1585 atoms, 1604 bonds, 118 residues, 1 model selected  

> delete sel

> select #18/E

1369 atoms, 1382 bonds, 1 pseudobond, 88 residues, 2 models selected  

> delete sel

> select #18/F

1550 atoms, 1566 bonds, 104 residues, 1 model selected  

> delete sel

> select add #18

7248 atoms, 7332 bonds, 1 pseudobond, 467 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.77662,0.181,0.60341,138.68,-0.45828,0.4949,-0.73828,134.8,-0.43226,-0.84989,-0.3014,190.01

> view matrix models
> #18,-0.80062,0.59389,-0.079453,117.09,0.044137,-0.073789,-0.9963,167.11,-0.59755,-0.80116,0.032864,186.57

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.80062,0.59389,-0.079453,119.76,0.044137,-0.073789,-0.9963,134.26,-0.59755,-0.80116,0.032864,132.67

> delete sel

> open 8pc2

Summary of feedback from opening 8pc2 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /C:16  
Atom H1 is not in the residue template for MET /D:1  
Atom H1 is not in the residue template for MET /E:16  
Atom H1 is not in the residue template for MET /F:1  
  
8pc2 title:  
SelDeg51 in complex with FKBP51FK1 domain and pVHL:EloB:EloC [more info...]  
  
Chain information for 8pc2 #18  
---  
Chain | Description | UniProt  
A B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
C E | Elongin-C | ELOC_HUMAN 17-112  
D F | Elongin-B | ELOB_HUMAN 1-104  
G H | Peptidyl-prolyl cis-trans isomerase FKBP5 | FKBP5_HUMAN 16-140  
  
Non-standard residues in 8pc2 #18  
---  
XZW —
[(1~{R})-3-(3,4-dimethoxyphenyl)-1-[4-[[1-[3-[2-[[[(2~{S},4~{R})-1-[(2~{S})-2-[(1-fluoranylcyclopropyl)carbonylamino]-3,3-dimethyl-
butanoyl]-4-oxidanyl-
pyrrolidin-2-yl]carbonylamino]methyl]-5-(4-methyl-1,3-thiazol-5-yl)phenoxy]propyl]-1,2,3-triazol-4-yl]methoxy]phenyl]propyl]
(2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate  
  
8pc2 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui mousemode right "translate selected models"

> select add #17

2 models selected  

> select subtract #17

Nothing selected  

> select add #18

14339 atoms, 14505 bonds, 2 pseudobonds, 934 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #18,1,0,0,38.073,0,1,0,177.57,0,0,1,134.03

> view matrix models #18,1,0,0,81.788,0,1,0,204.91,0,0,1,132.51

> ui mousemode right translate

> ui mousemode right "translate selected models"

> view matrix models #18,1,0,0,212.24,0,1,0,179.99,0,0,1,133.55

> hide sel atoms

> show sel cartoons

> color (#!18 & sel) hot pink

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.13447,-0.72061,0.68017,184.69,-0.91032,-0.18131,-0.37207,152.86,0.39144,-0.66921,-0.63161,135.41

> ui mousemode right "translate selected models"

> view matrix models
> #18,-0.13447,-0.72061,0.68017,184.63,-0.91032,-0.18131,-0.37207,153.56,0.39144,-0.66921,-0.63161,135.65

> view matrix models
> #18,-0.13447,-0.72061,0.68017,188.16,-0.91032,-0.18131,-0.37207,135.84,0.39144,-0.66921,-0.63161,96.836

> ui mousemode right "rotate selected models"

> view matrix models
> #18,-0.18052,-0.71423,0.67623,185.86,-0.56832,-0.48539,-0.66438,151.95,0.80276,-0.50425,-0.31828,118.18

> view matrix models
> #18,-0.0075376,-0.97404,-0.22623,182.92,-0.055407,0.2263,-0.97248,157.5,0.99844,0.0052047,-0.055674,122.59

> view matrix models
> #18,0.013282,0.24818,0.96862,182.61,-0.98845,-0.143,0.050191,138.83,0.15097,-0.9581,0.24341,106.01

> ui tool show Matchmaker

> matchmaker #!18 to #3/V pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain V (#3) with 8pc2, chain B (#18), sequence alignment
score = 612.8  
RMSD between 33 pruned atom pairs is 0.971 angstroms; (across all 37 pairs:
1.565)  
  

> show #!4 models

> select subtract #18

Nothing selected  

> ui mousemode right translate

> ui mousemode right "translate selected models"

> select ::name="XZW"

374 atoms, 392 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> hide #!7 models

> hide #!4 models

> select clear

> hide #!17 models

> show #!17 models

> select #18/B

2587 atoms, 2621 bonds, 157 residues, 1 model selected  

> select clear

> select #18/A

2575 atoms, 2613 bonds, 153 residues, 1 model selected  

> delete sel

> select #18/E

1369 atoms, 1382 bonds, 1 pseudobond, 88 residues, 2 models selected  

> delete sel

> select #18/D

1590 atoms, 1606 bonds, 104 residues, 1 model selected  

> select #18/F

1550 atoms, 1566 bonds, 104 residues, 1 model selected  

> delete sel

> select clear

> select #18/G

1724 atoms, 1740 bonds, 123 residues, 1 model selected  

> select clear

> select #18/H

1585 atoms, 1604 bonds, 118 residues, 1 model selected  

> delete sel

> select clear

> open 83wv

Fetching url http://files.rcsb.org/download/83wv.cif failed:  
HTTP Error 404: Not Found  

> open 8ewv

Summary of feedback from opening 8ewv fetched from pdb  
---  
note | Fetching compressed mmCIF 8ewv from
http://files.rcsb.org/download/8ewv.cif  
  
8ewv title:  
DNA-encoded library (DEL)-enabled discovery of proximity inducing small
molecules [more info...]  
  
Chain information for 8ewv #19  
---  
Chain | Description | UniProt  
A E I M Q U | Elongin-B | ELOB_HUMAN 1-118  
B F J N R V | Elongin-C | ELOC_HUMAN 17-112  
C G K O S W | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
D H L P T X | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 8ewv #19  
---  
X5K —
N-{3-[1-(4-{[3-(cyclopropylamino)-3-oxopropyl](methyl)amino}-6-{methyl[(1,3,5-trimethyl-1H-pyrazol-4-yl)methyl]amino}-1,3,5-triazin-2-yl)piperidin-4-yl]propanoyl}-3-methyl-
L-
valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide  
  
8ewv mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
3| author_defined_assembly  
4| author_defined_assembly  
5| author_defined_assembly  
6| author_defined_assembly  
  

> select add #19

22123 atoms, 22675 bonds, 6 pseudobonds, 2688 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #19,1,0,0,297.32,0,1,0,102.43,0,0,1,267.63

> ui mousemode right translate

> ui tool show Matchmaker

> matchmaker #!19 to #3/V pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain V (#3) with 8ewv, chain C (#19), sequence alignment
score = 624.8  
RMSD between 33 pruned atom pairs is 1.042 angstroms; (across all 37 pairs:
1.645)  
  

> matchmaker #!19 to #3/V pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain V (#3) with 8ewv, chain C (#19), sequence alignment
score = 624.8  
RMSD between 33 pruned atom pairs is 1.042 angstroms; (across all 37 pairs:
1.645)  
  

> hide sel atoms

> show sel cartoons

> select clear

> select ::name="X5K"

402 atoms, 438 bonds, 6 residues, 1 model selected  

> show sel atoms

> select clear

> select #19/K

1260 atoms, 1297 bonds, 147 residues, 1 model selected  

> delete sel

> select #19/W

1256 atoms, 1293 bonds, 147 residues, 1 model selected  

> delete sel

Drag select of 67 atoms, 537 residues, 1 pseudobonds, 73 bonds  

> delete sel

Drag select of 17 cryosparc_P14_J395_003_volume_map_sharp.mrc z flip , 134
atoms, 817 residues, 1 pseudobonds, 146 bonds  

> select subtract #17

6801 atoms, 146 bonds, 1 pseudobond, 819 residues, 2 models selected  

> delete sel

> select #19/G

353 atoms, 357 bonds, 2 pseudobonds, 41 residues, 2 models selected  

> delete sel

> select #19/C

1256 atoms, 1293 bonds, 147 residues, 1 model selected  

> select clear

> select #19/S

142 atoms, 144 bonds, 16 residues, 1 model selected  

> delete sel

Drag select of 93 residues, 5 pseudobonds  

> delete sel

Drag select of 2 pseudobonds  

> delete sel

> select clear

Drag select of 2 pseudobonds  

> delete sel

> select clear

Drag select of 17 cryosparc_P14_J395_003_volume_map_sharp.mrc z flip , 190
residues, 10 pseudobonds  

> select clear

> select #19/V

43 atoms, 43 bonds, 6 residues, 1 model selected  

> delete sel

> select #19/R

23 atoms, 20 bonds, 2 pseudobonds, 3 residues, 2 models selected  

> delete sel

> select #19/J

698 atoms, 713 bonds, 1 pseudobond, 90 residues, 2 models selected  

> delete sel

> select #19/F

603 atoms, 615 bonds, 2 pseudobonds, 77 residues, 2 models selected  

> delete sel

> select #19/B

706 atoms, 721 bonds, 1 pseudobond, 90 residues, 2 models selected  

> select #18/C

1359 atoms, 1373 bonds, 1 pseudobond, 87 residues, 2 models selected  

> select clear

> select #19/U

372 atoms, 371 bonds, 5 pseudobonds, 47 residues, 2 models selected  

> delete sel

> select #19/I

759 atoms, 774 bonds, 1 pseudobond, 97 residues, 2 models selected  

> delete sel

> select #19/E

545 atoms, 554 bonds, 3 pseudobonds, 68 residues, 2 models selected  

> delete sel

Drag select of 17 cryosparc_P14_J395_003_volume_map_sharp.mrc z flip , 51
residues, 2 pseudobonds  

> select subtract #17

414 atoms, 2 pseudobonds, 51 residues, 2 models selected  

> delete sel

> open 8bds

Summary of feedback from opening 8bds fetched from pdb  
---  
notes | Fetching compressed mmCIF 8bds from
http://files.rcsb.org/download/8bds.cif  
Fetching CCD SO4 from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/SO4/SO4.cif  
Fetching CCD EDO from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif  
Fetching CCD QIY from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/QIY/QIY.cif  
  
8bds title:  
Ternary complex between VCB, BRD4-BD1 and PROTAC 48 [more info...]  
  
Chain information for 8bds #20  
---  
Chain | Description | UniProt  
A | Elongin-B | ELOB_HUMAN 1-104  
B | Elongin-C | ELOC_HUMAN 17-112  
C | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
D | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 8bds #20  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
QIY —
(2~{S},4~{R})-~{N}-[(1~{S})-1-(4-chlorophenyl)-3-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethylamino]-3-oxidanylidene-
propyl]-1-[(2~{R})-3-methyl-2-(3-methyl-1,2-oxazol-5-yl)butanoyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
SO4 — sulfate ion  
  

> select add #20

4274 atoms, 3966 bonds, 1 pseudobond, 876 residues, 2 models selected  

> hide #!18 models

> hide #!19 models

> ui mousemode right "translate selected models"

> view matrix models #20,1,0,0,194.58,0,1,0,158.32,0,0,1,128.98

> view matrix models #20,1,0,0,166.57,0,1,0,215.73,0,0,1,136.45

> ui mousemode right translate

> ui tool show Matchmaker

> matchmaker #!20 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 8bds, chain C (#20), sequence alignment
score = 822.6  
RMSD between 147 pruned atom pairs is 0.548 angstroms; (across all 147 pairs:
0.548)  
  

> matchmaker #!20 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 8bds, chain C (#20), sequence alignment
score = 822.6  
RMSD between 147 pruned atom pairs is 0.548 angstroms; (across all 147 pairs:
0.548)  
  

> select clear

> open 7khh

Summary of feedback from opening 7khh fetched from pdb  
---  
note | Fetching compressed mmCIF 7khh from
http://files.rcsb.org/download/7khh.cif  
  
7khh title:  
Ternary complex of VHL/BRD4-BD1/Compound9
(4-(3,5-difluoropyridin-2-yl)-N-(11-(((S)-1-((2S,4R)-4-hydroxy-2-((4-(4-methylthiazol-5-yl)benzyl)carbamoyl)pyrrolidin-1-yl)-3,3-dimethyl-1-oxobutan-2-yl)amino)-11-oxoundecyl)-10-methyl-7-((methylsulfonyl)methyl)-11-oxo-3,4,10,11-tetrahydro-1H-1,4,10-triazadibenzo[cd,f]azulene-6-carboxamide)
[more info...]  
  
Chain information for 7khh #21  
---  
Chain | Description | UniProt  
A | Elongin-B | ELOB_HUMAN 1-118  
B | Elongin-C | ELOC_HUMAN 17-112  
C | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 55-213  
D | Bromodomain-containing protein 4 | BRD4_HUMAN 44-168  
  
Non-standard residues in 7khh #21  
---  
CSX — S-oxy cysteine  
WEP —
N-[11-({7-(3,5-difluoropyridin-2-yl)-2-methyl-10-[(methylsulfonyl)methyl]-3-oxo-3,4,6,7-tetrahydro-2H-2,4,7-triazadibenzo[cd,f]azulene-9-carbonyl}amino)undecanoyl]-3-methyl-
L-
valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide  
  

> ui tool show Matchmaker

> matchmaker #!21 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 7khh, chain C (#21), sequence alignment
score = 801.3  
RMSD between 148 pruned atom pairs is 0.456 angstroms; (across all 148 pairs:
0.456)  
  

> matchmaker #!21 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 7khh, chain C (#21), sequence alignment
score = 801.3  
RMSD between 148 pruned atom pairs is 0.456 angstroms; (across all 148 pairs:
0.456)  
  

> color #21 #fffb00ff

> save "/Users/ccrowe/OneDrive - University of Dundee/Documents/Biology/cryo-
> EM/CRL2/2023_11_16_mapCRL2/2023_11_24_chimeraxsession_withothersubs.cxs"
> includeMaps true

> open 6sis

Summary of feedback from opening 6sis fetched from pdb  
---  
notes | Fetching compressed mmCIF 6sis from
http://files.rcsb.org/download/6sis.cif  
Fetching CCD LFE from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/LFE/LFE.cif  
  
6sis title:  
Crystal structure of macrocyclic PROTAC 1 in complex with the second
bromodomain of human Brd4 and pVHL:ElonginC:ElonginB [more info...]  
  
Chain information for 6sis #22  
---  
Chain | Description | UniProt  
A E | Bromodomain-containing protein 4 | BRD4_HUMAN 333-460  
B F | Elongin-B | ELOB_HUMAN 1-104  
C G | Elongin-C | ELOC_HUMAN 17-112  
D H | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
  
Non-standard residues in 6sis #22  
---  
LFE —
~{N}-[(5~{S},7~{R},11~{S},23~{S})-11-~{tert}-butyl-34-(4-methyl-1,3-thiazol-5-yl)-7-oxidanyl-4,10,13-tris(oxidanylidene)-15,18,21,25,28,31-hexaoxa-3,9,12-triazatricyclo[30.4.0.0^{5,9}]hexatriaconta-1(32),33,35-trien-23-yl]-2-[(7~{S},9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanamide  
  
6sis mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!22 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 6sis, chain D (#22), sequence alignment
score = 822.6  
RMSD between 149 pruned atom pairs is 0.412 angstroms; (across all 149 pairs:
0.412)  
  

> matchmaker #!22 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 6sis, chain D (#22), sequence alignment
score = 822.6  
RMSD between 149 pruned atom pairs is 0.412 angstroms; (across all 149 pairs:
0.412)  
  

> select add #22

7369 atoms, 7546 bonds, 2 pseudobonds, 911 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #!20 models

> hide #!21 models

> hide #!17 models

> show #!17 models

> select ::name="SO4"

20 atoms, 16 bonds, 4 residues, 1 model selected  

> select clear

> select ::name="EDO"

24 atoms, 18 bonds, 6 residues, 1 model selected  

> select clear

> select ::name="LFE"

154 atoms, 168 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #22/E

885 atoms, 908 bonds, 111 residues, 1 model selected  

> delete sel

> select #22/H

1292 atoms, 1331 bonds, 150 residues, 1 model selected  

> delete sel

> select #22/G

689 atoms, 703 bonds, 1 pseudobond, 87 residues, 2 models selected  

> delete sel

> select #22/F

817 atoms, 833 bonds, 104 residues, 1 model selected  

> delete sel

> select clear

> open 7znt

Summary of feedback from opening 7znt fetched from pdb  
---  
notes | Fetching compressed mmCIF 7znt from
http://files.rcsb.org/download/7znt.cif  
Fetching CCD IZR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/IZR/IZR.cif  
  
7znt title:  
Crystal structure of AT7 In complex with the second bromodomain of human BRD4
and PVHL:elonginc:elonginb [more info...]  
  
Chain information for 7znt #23  
---  
Chain | Description | UniProt  
A D | Elongin-B | ELOB_HUMAN 1-104  
B E | Elongin-C | ELOC_HUMAN 17-112  
C F | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN 54-213  
G H | Bromodomain-containing protein 4 | BRD4_HUMAN 333-460  
  
Non-standard residues in 7znt #23  
---  
IZR —
(2~{S},4~{R})-1-[(2~{R})-3-[6-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]hexylsulfanyl]-2-[(1-fluoranylcyclopropyl)carbonylamino]-3-methyl-
butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
  
7znt mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> ui tool show Matchmaker

> matchmaker #!23 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 7znt, chain C (#23), sequence alignment
score = 799.2  
RMSD between 148 pruned atom pairs is 0.458 angstroms; (across all 149 pairs:
0.490)  
  

> matchmaker #!23 to #4/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5t35, chain D (#4) with 7znt, chain C (#23), sequence alignment
score = 799.2  
RMSD between 148 pruned atom pairs is 0.458 angstroms; (across all 149 pairs:
0.490)  
  

> select add #23

7333 atoms, 7482 bonds, 4 pseudobonds, 921 residues, 2 models selected  

> hide #!22 models

> hide sel atoms

> show sel cartoons

> select ::name="WEP"

81 atoms, 88 bonds, 1 residue, 1 model selected  

> select ::name="QIY"

71 atoms, 77 bonds, 1 residue, 1 model selected  

> select ::name="IZR"

138 atoms, 152 bonds, 2 residues, 1 model selected  

> show sel atoms

> select clear

> select #23/F

1279 atoms, 1309 bonds, 156 residues, 1 model selected  

> delete sel

> select #23/E

691 atoms, 702 bonds, 1 pseudobond, 89 residues, 2 models selected  

> delete sel

> select #23/D

765 atoms, 776 bonds, 1 pseudobond, 99 residues, 2 models selected  

> delete sel

> select #23/H

897 atoms, 919 bonds, 111 residues, 1 model selected  

> select #23/G

890 atoms, 911 bonds, 111 residues, 1 model selected  

> delete sel

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> show #!8 models

> hide #!8 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!16 models

> hide #!16 models

> show #!14 models

> hide #!14 models

> hide #!17 models

> show #!17 models

> hide #!23 models

> show #!4 models

> show #!3 models

> open 6ttu

6ttu title:  
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]  
  
Chain information for 6ttu #24  
---  
Chain | Description | UniProt  
C | Cullin-1 | CUL1_HUMAN 1-776  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN 1-147  
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |  
N | NEDD8 | NEDD8_HUMAN 1-76  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN 1-108  
S | S-phase kinase-associated protein 1 | SKP1_HUMAN 1-145  
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN 1-605  
U | Polyubiquitin-C | UBC_HUMAN 1-76  
  
Non-standard residues in 6ttu #24  
---  
ZN — zinc ion  
  

> select add #24

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #!24 to #3/R pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 6ttu, chain R (#24), sequence alignment
score = 461.5  
RMSD between 49 pruned atom pairs is 1.112 angstroms; (across all 77 pairs:
6.151)  
  

> matchmaker #24/R to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 6ttu, chain R (#24), sequence alignment
score = 461.5  
RMSD between 49 pruned atom pairs is 1.112 angstroms; (across all 77 pairs:
6.151)  
  

> matchmaker #24/R to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 6ttu, chain R (#24), sequence alignment
score = 461.5  
RMSD between 49 pruned atom pairs is 1.112 angstroms; (across all 77 pairs:
6.151)  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.65214,0.60199,-0.46078,247.01,-0.1752,-0.71104,-0.68098,435.72,-0.73758,-0.36336,0.56916,344.36

> view matrix models
> #24,-0.63481,0.76499,0.1087,115.75,0.57213,0.55992,-0.5993,82.934,-0.51932,-0.31825,-0.79311,541.88

> ui mousemode right "translate selected models"

> view matrix models
> #24,-0.63481,0.76499,0.1087,105.88,0.57213,0.55992,-0.5993,94.41,-0.51932,-0.31825,-0.79311,492.62

> view matrix models
> #24,-0.63481,0.76499,0.1087,136.55,0.57213,0.55992,-0.5993,105.61,-0.51932,-0.31825,-0.79311,487.62

> ui mousemode right "translate selected models"

> view matrix models
> #24,-0.63481,0.76499,0.1087,137.76,0.57213,0.55992,-0.5993,97.297,-0.51932,-0.31825,-0.79311,489.09

> ui mousemode right "rotate selected models"

> view matrix models
> #24,-0.63599,0.76676,0.087117,141.49,0.64527,0.59032,-0.48492,59.631,-0.42325,-0.25219,-0.87021,475.58

> ui mousemode right "translate selected models"

> view matrix models
> #24,-0.63599,0.76676,0.087117,140.79,0.64527,0.59032,-0.48492,65.754,-0.42325,-0.25219,-0.87021,476.75

> open 5ait

Summary of feedback from opening 5ait fetched from pdb  
---  
note | Fetching compressed mmCIF 5ait from
http://files.rcsb.org/download/5ait.cif  
  
5ait title:  
A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) [more
info...]  
  
Chain information for 5ait #25  
---  
Chain | Description | UniProt  
A | E3 UBIQUITIN-PROTEIN LIGASE RNF4 | RNF4_RAT 131-194 196-259  
B E | UBIQUITIN-CONJUGATING ENZYME E2 N | UBE2N_HUMAN 1-152  
C F | POLYUBIQUITIN-C | UBC_BOVIN 1-76  
D G | UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 2 | UB2V2_HUMAN 1-145  
  
Non-standard residues in 5ait #25  
---  
ZN — zinc ion  
  

> select subtract #24

Nothing selected  

> hide #!24 models

> ui tool show Matchmaker

> matchmaker #!25 to #3/R pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> matchmaker #!25 to #3/R pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> select add #25

6742 atoms, 6875 bonds, 16 pseudobonds, 855 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> ui tool show Matchmaker

> matchmaker #25/A to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> matchmaker #25/A to #3/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5n4w, chain R (#3) with 5ait, chain A (#25), sequence alignment
score = 82.7  
RMSD between 25 pruned atom pairs is 0.790 angstroms; (across all 72 pairs:
21.329)  
  

> select clear

> select #25/E

1173 atoms, 1203 bonds, 147 residues, 1 model selected  

> select clear

> hide #!25 models

> show #!24 models

> select add #24

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> hide #!17 models

> close #24

> show #!17 models

> show #!7 models

> select #7/R

669 atoms, 685 bonds, 13 pseudobonds, 82 residues, 3 models selected  

> color (#!7 & sel) medium blue

> select clear

> hide #!4 models

> hide #!3 models

> ui tool show Matchmaker

> matchmaker #25/A to #7/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ttu, chain R (#7) with 5ait, chain A (#25), sequence alignment
score = 89.3  
RMSD between 31 pruned atom pairs is 0.837 angstroms; (across all 50 pairs:
5.656)  
  

> matchmaker #25/A to #7/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ttu, chain R (#7) with 5ait, chain A (#25), sequence alignment
score = 89.3  
RMSD between 31 pruned atom pairs is 0.837 angstroms; (across all 50 pairs:
5.656)  
  

> show #!25 models

> hide #!7 models

> open 6nyo

6nyo title:  
Crystal structure of a human Cdc34-ubiquitin thioester mimetic [more info...]  
  
Chain information for 6nyo #24  
---  
Chain | Description | UniProt  
A | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN 1-202  
E | Ubiquitin |  
  
Non-standard residues in 6nyo #24  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
PO4 — phosphate ion  
U94 —
4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic
acid  
  

> ui tool show Matchmaker

> matchmaker #24 to #7/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ttu, chain D (#7) with 6nyo, chain A (#24), sequence alignment
score = 333.4  
RMSD between 113 pruned atom pairs is 1.226 angstroms; (across all 146 pairs:
1.958)  
  

> matchmaker #24 to #7/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ttu, chain D (#7) with 6nyo, chain A (#24), sequence alignment
score = 333.4  
RMSD between 113 pruned atom pairs is 1.226 angstroms; (across all 146 pairs:
1.958)  
  

> hide #24 models

> hide #!25 models

> hide #!17 models

> open /Users/ccrowe/Downloads/cryosparc_P14_J425_009_volume_map_sharp.mrc

Opened cryosparc_P14_J425_009_volume_map_sharp.mrc as #26, grid size
128,128,128, pixel 3.38, shown at level 0.158, step 1, values float32  

> open /Users/ccrowe/Downloads/cryosparc_P14_J409_009_volume_map_sharp.mrc

Opened cryosparc_P14_J409_009_volume_map_sharp.mrc as #27, grid size
128,128,128, pixel 3.38, shown at level 0.192, step 1, values float32  

> volume #26 level 0.4433

> volume #27 level 0.7354

> surface dust #26 size 33.8

> surface dust #27 size 33.8

> select add #27

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #27,0.92656,0.21156,-0.31103,45.037,0.13982,-0.9613,-0.23738,430.97,-0.34921,0.17646,-0.92028,489.13

> ui mousemode right "translate selected models"

> view matrix models
> #27,0.92656,0.21156,-0.31103,34.762,0.13982,-0.9613,-0.23738,437.75,-0.34921,0.17646,-0.92028,465.65

> select clear

> fitmap #26 inMap #27

Fit map cryosparc_P14_J425_009_volume_map_sharp.mrc in map
cryosparc_P14_J409_009_volume_map_sharp.mrc using 5304 points  
correlation = 0.4684, correlation about mean = 0.1235, overlap = 2971  
steps = 116, shift = 11.3, angle = 18.4 degrees  
  
Position of cryosparc_P14_J425_009_volume_map_sharp.mrc (#26) relative to
cryosparc_P14_J409_009_volume_map_sharp.mrc (#27) coordinates:  
Matrix rotation and translation  
0.99690210 0.01498710 -0.07721130 12.27385432  
0.03774770 -0.95239895 0.30250843 340.77892525  
-0.06900224 -0.30448584 -0.95001424 507.98636675  
Axis -0.99920647 -0.01351339 0.03746748  
Axis point 0.00000000 209.83848448 227.69702793  
Rotation angle (degrees) 162.31773513  
Shift along axis 2.16377737  
  

> select clear

> volume #26 level 0.4652

> volume #27 level 0.9165

> hide #!27 models

> hide #!26 models

> show #!26 models

> hide #!26 models

> show #!17 models

> volume #17 level 0.3048

> hide #!17 models

> show #!8 models

> hide #!8 models

> show #!8 models

> volume #8 level 0.1548

> show #9 models

> hide #9 models

> show #!12 models

> show #!13 models

> hide #!8 models

> hide #!13 models

> show #!13 models

> hide #!12 models

> volume #13.2 level -0.009403

> volume #13.2 level 0.01816

> show #!12 models

> hide #!13 models

> show #!13 models

> hide #!13 models

> hide #!12 models

> show #!13 models

> show #!12 models

> hide #!13 models

> hide #!12 models

> show #!17 models

> show #!26 models

> show #!27 models

> hide #!17 models

> hide #!27 models

> show #!27 models

> hide #!26 models

> show #!26 models

> hide #!27 models

> show #!27 models

> hide #!26 models

> hide #!27 models

> show #!17 models

> hide #!17 models

> show #!27 models

> show #!26 models

> hide #!27 models

> hide #!26 models

> show #!1 models

> show #!7 models

> hide #!7 models

> show #!11 models

> hide #!11 models

> show #!11 models

> hide #!11 models

> hide #!1 models

> show #!27 models

> show #!26 models

> hide #!27 models

> hide #!26 models

> show #!7 models

> select #7/I

58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected  

> hide #!7 models

> show #!7 models

> select add #7

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> select subtract #7

Nothing selected  

> hide #!7 models

> show #!17 models

> hide #!17 models

> show #!17 models

> show #!8 models

> transparency #8.1#17.1 0

> volume #8 level 0.1235

> volume #17 level 0.4251

> volume #17 level 0.2948

> hide #!17 models

> show #!18 models

> transparency #8.1 50

> hide #!18 models

> show #!4 models

> show #!18 models

> show #!19 models

> show #!20 models

> show #!21 models

> show #!22 models

> hide #!22 models

> hide #!21 models

> show #!21 models

> show #!22 models

> show #!23 models

> show #24 models

> hide #24 models

> hide #!23 models

> show #!23 models

> hide #!22 models

> show #!22 models

> hide #!23 models

> show #!23 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> show #!17 models

> hide #!8 models

> show #!8 models

> hide #!17 models

> show #9 models

> show #!3 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #!8 models

> show #!8 models

> volume #8 level 0.1938

> volume #8 level 0.1548

> hide #!4 models

> show #!4 models

> hide #!4 models

> show #!4 models

> hide #!3 models

> volume #8 level 0.186

> show #!3 models

> volume #8 level 0.1157

> show #!25 models

> hide #!25 models

> show #!25 models

> hide #!25 models

> show #24 models

> hide #24 models

> show #!7 models

> hide #!7 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #9 models

> show #9 models

> hide #9 models

> show #9 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> hide #!10 models

> volume #8 level 0.1001

> show #!3 models

> hide #!3 models

> show #!17 models

> hide #!8 models

> show #!8 models

> hide #9 models

> transparency #8.1#17.1 0

> transparency #8.1#17.1 50

> show #!10 models

> hide #!10 models

> show #!7 models

> hide #!7 models

> volume #17 level 0.2246

> hide #!17 models

> show #9 models

> volume #8 level 0.1313

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!5 models

> hide #!5 models

> show #6 models

> hide #6 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!25 models

> hide #!25 models

> show #!7 models

> show #!25 models

> show #!10 models

> hide #!10 models

> volume #16 level 0.2884

> volume #17 level 0.3248

> hide #!25 models

> hide #!7 models

> show #24 models

> hide #24 models

> show #!10 models

> hide #!10 models

> show #!7 models

> hide #!7 models

> show #!3 models

Unsupported scale factor (0.000000) detected on Display0  

QPainter::begin: Paint device returned engine == 0, type: 3  


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple

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: Mac14,9
      Model Number: Z17K001SWB/A
      Chip: Apple M2 Pro
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5.2 (22G91)
      Kernel Version: Darwin 22.6.0
      Time since boot: 4 days, 6 hours, 26 minutes

Graphics/Displays:

    Apple M2 Pro:

      Chipset Model: Apple M2 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 19
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        TH-65EQ2:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Online: Yes
          Rotation: Supported
          Television: Yes
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-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 (1)

comment:1 by Eric Pettersen, 2 years ago

Cc: Tom Goddard added
Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0
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