Opened 13 months ago

Closed 13 months ago

#15950 closed defect (can't reproduce)

Crash in event loop

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

Description (last modified by pett) 

The following bug report has been submitted:
Platform:        macOS-14.6.1-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: Aborted

Thread 0x0000000347a3b000 (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 0x0000000346a2f000 (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 0x0000000345a23000 (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 0x0000000344a17000 (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 0x0000000343a0b000 (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 0x00000003429ff000 (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 0x00000003419f3000 (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 0x00000003409e7000 (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 0x000000033f9db000 (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 0x000000033e9cf000 (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 0x000000033d9c3000 (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 0x000000033c9b7000 (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 0x00000003377cb000 (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 0x00000001fe3dcf40 (most recent call first):
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
  File "/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main


{"app_name":"ChimeraX","timestamp":"2024-09-16 13:35:16.00 +0200","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":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"A070D234-2667-4584-A2B1-0B7E025F1BDA"}
{
  "uptime" : 280000,
  "procRole" : "Foreground",
  "version" : 2,
  "userID" : 501,
  "deployVersion" : 210,
  "modelCode" : "MacBookPro18,2",
  "coalitionID" : 751,
  "osVersion" : {
    "train" : "macOS 14.6.1",
    "build" : "23G93",
    "releaseType" : "User"
  },
  "captureTime" : "2024-09-16 13:35:11.7400 +0200",
  "codeSigningMonitor" : 1,
  "incident" : "A070D234-2667-4584-A2B1-0B7E025F1BDA",
  "pid" : 29236,
  "translated" : false,
  "cpuType" : "ARM-64",
  "roots_installed" : 0,
  "bug_type" : "309",
  "procLaunch" : "2024-09-11 14:53:07.4999 +0200",
  "procStartAbsTime" : 4683978121625,
  "procExitAbsTime" : 6861724196454,
  "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":"6B960448-CE3F-59C7-9F4B-4A688BB3DBC6","thirdParty":true},
  "parentProc" : "launchd",
  "parentPid" : 1,
  "coalitionName" : "edu.ucsf.cgl.ChimeraX",
  "crashReporterKey" : "00676DF6-615F-3E8F-4E81-80128E8B8F44",
  "codeSigningID" : "edu.ucsf.cgl.ChimeraX",
  "codeSigningTeamID" : "LWV8X224YF",
  "codeSigningFlags" : 570491649,
  "codeSigningValidationCategory" : 6,
  "codeSigningTrustLevel" : 4294967295,
  "instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
  "wakeTime" : 16488,
  "sleepWakeUUID" : "9A101611-A6C7-47C9-832F-0D0FDA757E96",
  "sip" : "enabled",
  "exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
  "termination" : {"flags":0,"code":6,"namespace":"SIGNAL","indicator":"Abort trap: 6","byProc":"ChimeraX","byPid":29236},
  "asi" : {"libsystem_c.dylib":["abort() called"]},
  "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" : 44,
  "threads" : [{"threadState":{"x":[{"value":105553135388032},{"value":105553135388032},{"value":259},{"value":0},{"value":20017942},{"value":12640},{"value":4},{"value":0},{"value":8560541696,"symbolLocation":0,"symbol":"LSSharedMemoryPage::getSharedMemoryPageRefs()::sDict"},{"value":1239685332636532863},{"value":52180},{"value":8565577984,"symbolLocation":0,"symbol":"__CFRuntimeClassTables"},{"value":0},{"value":2095104},{"value":2043},{"value":2733273484},{"value":6822892780,"symbolLocation":0,"symbol":"_LSGetCurrentApplicationASN"},{"value":8591668104},{"value":0},{"value":105553695197632},{"value":8591442760},{"value":29},{"value":105553672188256},{"value":18446744073709551615},{"value":0},{"value":0},{"value":105553672165376},{"value":29},{"value":1}],"flavor":"ARM_THREAD_STATE64","lr":{"value":10316902328264508916},"cpsr":{"value":1610616832},"fp":{"value":6123380880},"sp":{"value":6123380704},"esr":{"value":1442840704,"description":" Address size 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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  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_16/RBP_55_cluster_16.pdb

Chain information for RBP_55_cluster_16.pdb #1  
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Chain | Description  
A B C | No description available  
  

> close

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_15/RBP_30_cluster_15.pdb

Chain information for RBP_30_cluster_15.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_15/RBP_32_cluster_15.pdb

Chain information for RBP_32_cluster_15.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
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Chain information for RBP_53_cluster_15.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> tile

3 models tiled  

> close

> open /Users/shj152/Library/CloudStorage/OneDrive-
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Chain information for RBP_25_cluster_14.pdb #1  
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Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
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Chain information for RBP_29_cluster_14.pdb #2  
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Chain | Description  
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> tile

2 models tiled  

> close

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_13/RBP_12_cluster_13.pdb

Chain information for RBP_12_cluster_13.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_13/RBP_61_cluster_13.pdb

Chain information for RBP_61_cluster_13.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> close

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/filtered_new/cluster_11/RBP_14_cluster_11.pdb

Chain information for RBP_14_cluster_11.pdb #1  
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Chain | Description  
A B C | No description available  
  

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> open
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---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right translate

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> open
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Chain information for RBP_00_relax_domain_12.pdb #1  
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Chain | Description  
A B C | No description available  
  

> open
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Chain information for RBP_00_relax_domain_13.pdb #2  
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Chain | Description  
A B C | No description available  
  

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Chain information for RBP_00_relax_domain_10.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
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Chain information for RBP_00_relax_domain_11.pdb #4  
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Chain | Description  
A B C | No description available  
  

> open
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Chain information for RBP_00_relax_domain_9.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

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Chain information for RBP_00_relax_domain_8.pdb #6  
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Chain | Description  
A B C | No description available  
  

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Chain information for RBP_00_relax_domain_7.pdb #7  
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Chain | Description  
A B C | No description available  
  

> open
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Chain information for RBP_00_relax_domain_6.pdb #8  
---  
Chain | Description  
A B C | No description available  
  

> open
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Chain information for RBP_00_relax_domain_5.pdb #9  
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Chain | Description  
A B C | No description available  
  

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Chain | Description  
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Chain information for RBP_00_relax_domain_3.pdb #11  
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Chain | Description  
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Chain information for RBP_00_relax_domain_1.pdb #12  
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Chain | Description  
A B C | No description available  
  

> open
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Chain information for RBP_00_relax_domain_2.pdb #13  
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Chain | Description  
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> ui mousemode right translate

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Chain information for RBP_01_relax_domain_16.pdb #1  
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Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_15.pdb

Chain information for RBP_01_relax_domain_15.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_13.pdb

Chain information for RBP_01_relax_domain_13.pdb #3  
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Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_14.pdb

Chain information for RBP_01_relax_domain_14.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_12.pdb

Chain information for RBP_01_relax_domain_12.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_10.pdb

Chain information for RBP_01_relax_domain_10.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_11.pdb

Chain information for RBP_01_relax_domain_11.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_8.pdb

Chain information for RBP_01_relax_domain_8.pdb #8  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_9.pdb

Chain information for RBP_01_relax_domain_9.pdb #9  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_7.pdb

Chain information for RBP_01_relax_domain_7.pdb #10  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_6.pdb

Chain information for RBP_01_relax_domain_6.pdb #11  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_5.pdb

Chain information for RBP_01_relax_domain_5.pdb #12  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_4.pdb

Chain information for RBP_01_relax_domain_4.pdb #13  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_3.pdb

Chain information for RBP_01_relax_domain_3.pdb #14  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_2.pdb

Chain information for RBP_01_relax_domain_2.pdb #15  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_01_relax_domain_1.pdb

Chain information for RBP_01_relax_domain_1.pdb #16  
---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right zoom

> close #1,3,6,8,12-14#2,4-5,7,9-11,15-16

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_17.pdb

Chain information for RBP_02_relax_domain_17.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_18.pdb

Chain information for RBP_02_relax_domain_18.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_16.pdb

Chain information for RBP_02_relax_domain_16.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_15.pdb

Chain information for RBP_02_relax_domain_15.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_14.pdb

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_13.pdb

Chain information for RBP_02_relax_domain_13.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_12.pdb

Chain information for RBP_02_relax_domain_12.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_10.pdb

Chain information for RBP_02_relax_domain_10.pdb #8  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_11.pdb

Chain information for RBP_02_relax_domain_11.pdb #9  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_9.pdb

Chain information for RBP_02_relax_domain_9.pdb #10  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_8.pdb

Chain information for RBP_02_relax_domain_8.pdb #11  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_7.pdb

Chain information for RBP_02_relax_domain_7.pdb #12  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_5.pdb

Chain information for RBP_02_relax_domain_5.pdb #13  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_6.pdb

Chain information for RBP_02_relax_domain_6.pdb #14  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_4.pdb

Chain information for RBP_02_relax_domain_4.pdb #15  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_3.pdb

Chain information for RBP_02_relax_domain_3.pdb #16  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_2.pdb

Chain information for RBP_02_relax_domain_2.pdb #17  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_1.pdb

Chain information for RBP_02_relax_domain_1.pdb #18  
---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right select

Drag select of 2 residues  

> select up

224 atoms, 223 bonds, 15 residues, 1 model selected  

> ui mousemode right zoom

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_6.pdb

Chain information for RBP_06_relax_domain_6.pdb #19  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_7.pdb

Chain information for RBP_06_relax_domain_7.pdb #20  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_5.pdb

Chain information for RBP_06_relax_domain_5.pdb #21  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_4.pdb

Chain information for RBP_06_relax_domain_4.pdb #22  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_3.pdb

Chain information for RBP_06_relax_domain_3.pdb #23  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_2.pdb

Chain information for RBP_06_relax_domain_2.pdb #24  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_1.pdb

Chain information for RBP_06_relax_domain_1.pdb #25  
---  
Chain | Description  
A B C | No description available  
  

> close #1-2,4-5,10,13,19-25#3,6-9,11-12,14-18

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_6.pdb

Chain information for RBP_06_relax_domain_6.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_7.pdb

Chain information for RBP_06_relax_domain_7.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_5.pdb

Chain information for RBP_06_relax_domain_5.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_4.pdb

Chain information for RBP_06_relax_domain_4.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_3.pdb

Chain information for RBP_06_relax_domain_3.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_2.pdb

Chain information for RBP_06_relax_domain_2.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_1.pdb

Chain information for RBP_06_relax_domain_1.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right translate

> close

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_12.pdb

Chain information for RBP_00_relax_domain_12.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_13.pdb

Chain information for RBP_00_relax_domain_13.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_11.pdb

Chain information for RBP_00_relax_domain_11.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_10.pdb

Chain information for RBP_00_relax_domain_10.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_9.pdb

Chain information for RBP_00_relax_domain_9.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_8.pdb

Chain information for RBP_00_relax_domain_8.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_7.pdb

Chain information for RBP_00_relax_domain_7.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_6.pdb

Chain information for RBP_00_relax_domain_6.pdb #8  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_5.pdb

Chain information for RBP_00_relax_domain_5.pdb #9  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_4.pdb

Chain information for RBP_00_relax_domain_4.pdb #10  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_3.pdb

Chain information for RBP_00_relax_domain_3.pdb #11  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_2.pdb

Chain information for RBP_00_relax_domain_2.pdb #12  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_00_relax_domain_1.pdb

Chain information for RBP_00_relax_domain_1.pdb #13  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_6.pdb

Chain information for RBP_02_relax_domain_6.pdb #14  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_5.pdb

Chain information for RBP_02_relax_domain_5.pdb #15  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_3.pdb

Chain information for RBP_02_relax_domain_3.pdb #16  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_4.pdb

Chain information for RBP_02_relax_domain_4.pdb #17  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_2.pdb

Chain information for RBP_02_relax_domain_2.pdb #18  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_02_relax_domain_1.pdb

Chain information for RBP_02_relax_domain_1.pdb #19  
---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right zoom

> close #1-4,6-9,11#5,10,12-13

> close #14,16,18-19#15,17

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_4.pdb

Chain information for RBP_03_relax_domain_4.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_5.pdb

Chain information for RBP_03_relax_domain_5.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_3.pdb

Chain information for RBP_03_relax_domain_3.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_1.pdb

Chain information for RBP_03_relax_domain_1.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_03_relax_domain_2.pdb

Chain information for RBP_03_relax_domain_2.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right select

Drag select of 334 residues  

> select up

4539 atoms, 4596 bonds, 336 residues, 1 model selected  

> select up

6564 atoms, 6645 bonds, 489 residues, 1 model selected  

> close #1-2,4#3,5

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_3.pdb

Chain information for RBP_06_relax_domain_3.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_4.pdb

Chain information for RBP_06_relax_domain_4.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_2.pdb

Chain information for RBP_06_relax_domain_2.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_06_relax_domain_1.pdb

Chain information for RBP_06_relax_domain_1.pdb #4  
---  
Chain | Description  
A B C | No description available  
  
Drag select of 8 residues  

> select clear

> ui mousemode right zoom

> ui mousemode right translate

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_12_relax_domain_3.pdb

Chain information for RBP_12_relax_domain_3.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_12_relax_domain_2.pdb

Chain information for RBP_12_relax_domain_2.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_12_relax_domain_1.pdb

Chain information for RBP_12_relax_domain_1.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> hide #4 models

> hide #3 models

> hide #2 models

> hide #1 models

> close

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_16_relax_domain_2.pdb

Chain information for RBP_16_relax_domain_2.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_16_relax_domain_1.pdb

Chain information for RBP_16_relax_domain_1.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> ui mousemode right zoom

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_6.pdb

Chain information for RBP_04_relax_domain_6.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_4.pdb

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_3.pdb

Chain information for RBP_04_relax_domain_3.pdb #5  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_2.pdb

Chain information for RBP_04_relax_domain_2.pdb #6  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_1.pdb

Chain information for RBP_04_relax_domain_1.pdb #7  
---  
Chain | Description  
A B C | No description available  
  

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_04_relax_domain_5.pdb

Chain information for RBP_04_relax_domain_5.pdb #8  
---  
Chain | Description  
A B C | No description available  
  

> hide #!1 models

> hide #!2 models

> close #3-8#1-2

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_14_relax_domain_1.pdb

Chain information for RBP_14_relax_domain_1.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> close #1

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_60_relax_domain_2.pdb

Chain information for RBP_60_relax_domain_2.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> close #1

> open
> /private/var/folders/2p/8071jp1s2ml2vj_81_qt_5680000gn/T/fz3temp-3/RBP_64_relax_domain_4.pdb

Chain information for RBP_64_relax_domain_4.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> close #1

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_15_cluster_17.pdb

Chain information for RBP_15_cluster_17.pdb #1  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_40_cluster_17.pdb

Chain information for RBP_40_cluster_17.pdb #2  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_46_cluster_17.pdb

Chain information for RBP_46_cluster_17.pdb #3  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/nick/seq_clusters/cluster_17/RBP_47_cluster_17.pdb

Chain information for RBP_47_cluster_17.pdb #4  
---  
Chain | Description  
A B C | No description available  
  

> close

> open /Users/shj152/Downloads/uniparc_YP_009966082_2024_09_16.tsv

Install the ArtiaX bundle to open "Generic Particle List" format files.  

Failed opening file
/Users/shj152/Downloads/uniparc_YP_009966082_2024_09_16.tsv:  
Opener for format 'Generic Particle List' is not installed; see log for more
info  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/docs/fig/bas49_bas54.cxs

Opened cryosparc_P310_J84_class_00_00041_volume.mrc as #1, grid size
128,128,128, pixel 7.03, shown at level 2.07, step 1, values float32  
Opened cryosparc_P310_J88_001_volume_map_sharp.mrc as #7, grid size
300,300,300, pixel 3, shown at level 0.439, step 1, values float32  
Opened cryosparc_P310_J88_001_volume_map_sharp(1).mrc as #9, grid size
300,300,300, pixel 3, shown at level 0.939, step 1, values float32  
Opened cryosparc_P310_J114_002_volume_map.mrc as #8, grid size 300,300,300,
pixel 3, shown at level 0.424, step 1, values float32  
Opened cryosparc_P310_J184_class_00_00062_volume.mrc as #11, grid size
128,128,128, pixel 5.06, shown at level 1.3, step 1, values float32  
Opened cryosparc_P310_J187_003_volume_map.mrc as #12, grid size 300,300,300,
pixel 2.16, shown at level 0.242, step 1, values float32  
Opened cryosparc_P310_J129_002_volume_map_sharp.mrc as #13, grid size
300,300,300, pixel 4.8, shown at level 1.6, step 1, values float32  
Opened cryosparc_P310_J320_002_volume_map.mrc as #14, grid size 208,208,208,
pixel 4.62, shown at level 0.966, step 1, values float32  
Opened cryosparc_P310_J305_002_volume_map.mrc as #15, grid size 208,208,208,
pixel 4.62, shown at level 0.922, step 1, values float32  
Opened cryosparc_P310_J310_007_volume_map.mrc as #34, grid size 300,300,300,
pixel 3.6, shown at level 0.141, step 2, values float32  
Opened cryosparc_P310_J310_007_volume_map.mrc z flip as #35, grid size
300,300,300, pixel 3.6, shown at level 1.07, step 1, values float32  
opened ChimeraX session  

> ui mousemode right translate

> hide #30 models

> show #30 models

> hide #31 models

> show #31 models

> show #29 models

> color #13 white models

> color #13 #ffffff33 models

> color #14 white models

> color #14 #ffffff33 models

> color #14 #ffffff05 models

> color #13 #ffffff05 models

> color #13 #ffffff33 models

> color #14 #ffffff33 models

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/cluster_D4/RBP_65_1__cluster_D4_TCTC8_.pdb

Chain information for RBP_65_1__cluster_D4_TCTC8_.pdb #46  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/highconfidence/cluster_D34/RBP_65_2__cluster_D34_TCTC8_.pdb

Chain information for RBP_65_2__cluster_D34_TCTC8_.pdb #47  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/highconfidence/cluster_D12/RBP_65_3__cluster_D12_TCTC8_.pdb

Chain information for RBP_65_3__cluster_D12_TCTC8_.pdb #48  
---  
Chain | Description  
A B C | No description available  
  

> open /Users/shj152/Library/CloudStorage/OneDrive-
> UniversityofCopenhagen/PhD/AtlasPaper/data/240410/newmerge_040424/USscore/pdb_files/renamed/domains_50/new_240912/highconfidence/cluster_D15/RBP_65_4__cluster_D15_TCTC8_.pdb

Chain information for RBP_65_4__cluster_D15_TCTC8_.pdb #49  
---  
Chain | Description  
A B C | No description available  
  

> show #5 models

> hide #5 models

> mmaker #46-49 to #5

Parameters  
---  
Chain pairing | bb  
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 RBP_65_cluster_8.pdb, chain B (#5) with
RBP_65_1__cluster_D4_TCTC8_.pdb, chain B (#46), sequence alignment score =
623.7  
RMSD between 121 pruned atom pairs is 0.000 angstroms; (across all 121 pairs:
0.000)  
  
Matchmaker RBP_65_cluster_8.pdb, chain C (#5) with
RBP_65_2__cluster_D34_TCTC8_.pdb, chain C (#47), sequence alignment score =
974.9  
RMSD between 190 pruned atom pairs is 0.000 angstroms; (across all 190 pairs:
0.000)  
  
Matchmaker RBP_65_cluster_8.pdb, chain C (#5) with
RBP_65_3__cluster_D12_TCTC8_.pdb, chain C (#48), sequence alignment score =
628.7  
RMSD between 124 pruned atom pairs is 0.000 angstroms; (across all 124 pairs:
0.000)  
  
Matchmaker RBP_65_cluster_8.pdb, chain B (#5) with
RBP_65_4__cluster_D15_TCTC8_.pdb, chain B (#49), sequence alignment score =
753.3  
RMSD between 146 pruned atom pairs is 0.000 angstroms; (across all 146 pairs:
0.000)  
  

> hide #!14 models

> show #!14 models

> hide #!13 models

> show #!13 models

> select add #46

5616 atoms, 5700 bonds, 363 residues, 1 model selected  

> select add #47

14214 atoms, 14388 bonds, 933 residues, 2 models selected  

> fitmap sel inMap #13

Fit molecules RBP_65_1__cluster_D4_TCTC8_.pdb (#46),
RBP_65_2__cluster_D34_TCTC8_.pdb (#47) to map
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) using 14214 atoms  
average map value = 1.693, steps = 324  
shifted from previous position = 7.07  
rotated from previous position = 38.1 degrees  
atoms outside contour = 5075, contour level = 1.5981  
  
Position of RBP_65_1__cluster_D4_TCTC8_.pdb (#46) relative to
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.08020332 0.46207192 0.88320833 787.49707441  
0.93966459 0.26057454 -0.22165597 680.37266050  
-0.33256261 0.84769714 -0.41329368 798.79993278  
Axis 0.63346237 0.72019722 0.28291588  
Axis point 268.12464024 0.00000000 258.92186386  
Rotation angle (degrees) 122.42925976  
Shift along axis 1214.84544472  
  
Position of RBP_65_2__cluster_D34_TCTC8_.pdb (#47) relative to
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.08020333 0.46207193 0.88320833 787.49707456  
0.93966458 0.26057454 -0.22165598 680.37266110  
-0.33256261 0.84769714 -0.41329368 798.79993335  
Axis 0.63346237 0.72019722 0.28291588  
Axis point 268.12464109 0.00000000 258.92186690  
Rotation angle (degrees) 122.42925958  
Shift along axis 1214.84544391  
  

> select subtract #46

8598 atoms, 8688 bonds, 570 residues, 1 model selected  

> select subtract #47

Nothing selected  

> select add #48

5418 atoms, 5445 bonds, 372 residues, 1 model selected  

> select add #49

11913 atoms, 12012 bonds, 810 residues, 2 models selected  

> fitmap sel inMap #14

Fit molecules RBP_65_3__cluster_D12_TCTC8_.pdb (#48),
RBP_65_4__cluster_D15_TCTC8_.pdb (#49) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 11913 atoms  
average map value = 1.483, steps = 320  
shifted from previous position = 1.23  
rotated from previous position = 61.4 degrees  
atoms outside contour = 2738, contour level = 0.96601  
  
Position of RBP_65_3__cluster_D12_TCTC8_.pdb (#48) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.94832432 0.00499779 0.31726332 501.68355928  
0.28105700 0.47729871 0.83258207 720.05619692  
-0.14726830 0.87872690 -0.45403864 667.90439830  
Axis 0.08508541 0.85653941 0.50901937  
Axis point 227.91704534 0.00000000 86.39106593  
Rotation angle (degrees) 164.26623707  
Shift along axis 999.41873464  
  
Position of RBP_65_4__cluster_D15_TCTC8_.pdb (#49) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.94832432 0.00499780 0.31726331 501.68356164  
0.28105700 0.47729871 0.83258207 720.05619701  
-0.14726829 0.87872690 -0.45403864 667.90439787  
Axis 0.08508541 0.85653941 0.50901937  
Axis point 227.91704447 0.00000000 86.39106791  
Rotation angle (degrees) 164.26623779  
Shift along axis 999.41873592  
  

> hide #29 models

> hide #30 models

> hide #31 models

> hide #32 models

> color #46 lightpink

> color #47 lightpink

> color #48 lightpink

> color #49 lightpink

> ui mousemode right select

> select clear

> select add #48

5418 atoms, 5445 bonds, 372 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #48,-0.77681,0.018412,0.62947,419.9,-0.55339,-0.49701,-0.66839,611.79,0.30054,-0.86755,0.39627,490.94

> view matrix models
> #48,-0.79306,0.067894,0.60534,424.58,-0.52916,-0.56904,-0.62943,605.18,0.30173,-0.8195,0.48721,501.34

> fitmap sel inMap #14

Fit molecule RBP_65_3__cluster_D12_TCTC8_.pdb (#48) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 5418 atoms  
average map value = 1.818, steps = 184  
shifted from previous position = 66.9  
rotated from previous position = 10.1 degrees  
atoms outside contour = 544, contour level = 0.96601  
  
Position of RBP_65_3__cluster_D12_TCTC8_.pdb (#48) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.83262730 -0.10089186 0.54456644 493.31064875  
0.43446374 0.49080692 0.75521509 665.37974065  
-0.34347203 0.86540707 -0.36482539 629.91961602  
Axis 0.10567282 0.85161845 0.51339972  
Axis point 229.52221678 0.00000000 49.36187477  
Rotation angle (degrees) 148.57494528  
Shift along axis 942.17974308  
  

> view matrix models
> #48,-0.78484,0.043217,0.6182,422.29,-0.54141,-0.53317,-0.65008,608.41,0.30151,-0.84491,0.44185,495.98

> view matrix models
> #48,-0.79449,0.072103,0.60298,424.96,-0.52703,-0.57515,-0.62565,604.64,0.30169,-0.81487,0.49495,502.29

> view matrix models
> #48,-0.79449,0.072103,0.60298,425.37,-0.52703,-0.57515,-0.62565,605.14,0.30169,-0.81487,0.49495,502.72

> view matrix models
> #48,-0.8009,0.036131,0.59771,420.84,-0.50476,-0.57775,-0.64142,603.96,0.32215,-0.81541,0.48095,501.88

> fitmap sel inMap #14

Fit molecule RBP_65_3__cluster_D12_TCTC8_.pdb (#48) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 5418 atoms  
average map value = 1.818, steps = 200  
shifted from previous position = 66.4  
rotated from previous position = 10.6 degrees  
atoms outside contour = 535, contour level = 0.96601  
  
Position of RBP_65_3__cluster_D12_TCTC8_.pdb (#48) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.84352364 -0.09625942 0.52839567 493.11002571  
0.42437878 0.48354720 0.76556173 665.12522520  
-0.32919678 0.87000933 -0.36703304 630.17119592  
Axis 0.10354865 0.85021139 0.51615721  
Axis point 228.97741272 0.00000000 50.22748700  
Rotation angle (degrees) 149.71240237  
Shift along axis 941.82532701  
  

> select subtract #48

Nothing selected  

> select add #49

6495 atoms, 6567 bonds, 438 residues, 1 model selected  

> view matrix models
> #49,-0.88832,0.11619,0.44429,422.75,-0.45112,-0.40185,-0.79687,616.21,0.085946,-0.9083,0.40939,487.36

> fitmap sel inMap #14

Fit molecule RBP_65_4__cluster_D15_TCTC8_.pdb (#49) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 6495 atoms  
average map value = 1.793, steps = 52  
shifted from previous position = 1.64  
rotated from previous position = 11.3 degrees  
atoms outside contour = 346, contour level = 0.96601  
  
Position of RBP_65_4__cluster_D15_TCTC8_.pdb (#49) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.90994301 0.06014993 0.41034827 522.13653224  
0.40627866 0.32804507 0.85283298 691.25930910  
-0.08331488 0.94274515 -0.32293996 693.43280601  
Axis 0.14749761 0.80983619 0.56781141  
Axis point 208.55320623 0.00000000 68.70579107  
Rotation angle (degrees) 162.25435089  
Shift along axis 1030.55975395  
  

> select subtract #49

Nothing selected  

> show #5 models

> hide #46 models

> hide #47 models

> hide #48 models

> hide #49 models

> select add #5

26127 atoms, 26409 bonds, 1743 residues, 1 model selected  

> fitmap sel inMap #14

Fit molecule RBP_65_cluster_8.pdb (#5) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms  
average map value = 0.9266, steps = 44  
shifted from previous position = 0.11  
rotated from previous position = 0.692 degrees  
atoms outside contour = 17957, contour level = 0.96601  
  
Position of RBP_65_cluster_8.pdb (#5) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.23090830 -0.19491842 0.95325136 511.52670757  
0.57417104 0.76365264 0.29523254 728.53549205  
-0.78549919 0.61550097 -0.06441722 652.45436137  
Axis 0.16611120 0.90182460 0.39889781  
Axis point 295.35000064 0.00000000 19.41360326  
Rotation angle (degrees) 105.41666021  
Shift along axis 1002.24416035  
  

> fitmap sel inMap #13

Fit molecule RBP_65_cluster_8.pdb (#5) to map
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) using 26127 atoms  
average map value = 1.47, steps = 520  
shifted from previous position = 1.63  
rotated from previous position = 24.4 degrees  
atoms outside contour = 14806, contour level = 1.5981  
  
Position of RBP_65_cluster_8.pdb (#5) relative to
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.20469403 0.47569544 0.85546139 788.07259516  
0.84420051 0.35653687 -0.40025859 680.30836126  
-0.49540472 0.80411149 -0.32860137 799.83935798  
Axis 0.65209373 0.73141249 0.19952326  
Axis point 349.08428464 0.00000000 295.98470877  
Rotation angle (degrees) 112.56214208  
Shift along axis 1171.06979176  
  

> fitmap sel inMap #14

Fit molecule RBP_65_cluster_8.pdb (#5) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms  
average map value = 0.9435, steps = 96  
shifted from previous position = 1.31  
rotated from previous position = 4.53 degrees  
atoms outside contour = 17676, contour level = 0.96601  
  
Position of RBP_65_cluster_8.pdb (#5) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.63901010 -0.12361064 0.75920123 511.53084314  
0.52127249 0.65620632 0.54558983 729.06550456  
-0.56563335 0.74438812 -0.35488764 653.25955497  
Axis 0.13370861 0.89106292 0.43373826  
Axis point 255.78677255 0.00000000 54.79414877  
Rotation angle (degrees) 131.97803835  
Shift along axis 1001.38297857  
  

> fitmap sel inMap #13

Fit molecule RBP_65_cluster_8.pdb (#5) to map
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) using 26127 atoms  
average map value = 1.481, steps = 56  
shifted from previous position = 1.24  
rotated from previous position = 3.91 degrees  
atoms outside contour = 14656, contour level = 1.5981  
  
Position of RBP_65_cluster_8.pdb (#5) relative to
cryosparc_P310_J129_002_volume_map_sharp.mrc (#13) coordinates:  
Matrix rotation and translation  
0.15430263 0.46883794 0.86970206 787.99411508  
0.88234957 0.33069254 -0.33481589 680.35358621  
-0.44457837 0.81904421 -0.36265223 799.72510786  
Axis 0.64205296 0.73131711 0.23009406  
Axis point 320.14205827 0.00000000 281.92088963  
Rotation angle (degrees) 116.02916070  
Shift along axis 1187.50017396  
  

> fitmap sel inMap #14

Fit molecule RBP_65_cluster_8.pdb (#5) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms  
average map value = 0.9469, steps = 60  
shifted from previous position = 1.21  
rotated from previous position = 3.94 degrees  
atoms outside contour = 17619, contour level = 0.96601  
  
Position of RBP_65_cluster_8.pdb (#5) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.68582226 -0.10802606 0.71970702 511.47347502  
0.50424604 0.64254559 0.57694981 729.04683610  
-0.52477019 0.75859444 -0.38620036 653.38306737  
Axis 0.12985899 0.88968533 0.43771755  
Axis point 251.86171359 0.00000000 59.90565334  
Rotation angle (degrees) 135.62177335  
Shift along axis 1001.03894125  
  

> view matrix models
> #5,-0.60188,0.037193,0.79772,433.36,-0.65543,-0.59369,-0.46684,608.02,0.45624,-0.80383,0.38171,501.82

> view matrix models
> #5,-0.04817,-0.055293,0.99731,432.81,-0.61675,-0.78375,-0.073241,608.76,0.78569,-0.61861,0.0036515,500.47

> fitmap sel inMap #14

Fit molecule RBP_65_cluster_8.pdb (#5) to map
cryosparc_P310_J320_002_volume_map.mrc (#14) using 26127 atoms  
average map value = 0.9243, steps = 68  
shifted from previous position = 4.1  
rotated from previous position = 2.04 degrees  
atoms outside contour = 17975, contour level = 0.96601  
  
Position of RBP_65_cluster_8.pdb (#5) relative to
cryosparc_P310_J320_002_volume_map.mrc (#14) coordinates:  
Matrix rotation and translation  
-0.13035021 -0.20085621 0.97090968 511.20698497  
0.56875803 0.78696620 0.23916208 728.10289116  
-0.81211029 0.58338751 0.01165737 652.20126182  
Axis 0.17453018 0.90403196 0.39021205  
Axis point 307.52978038 0.00000000 11.61714579  
Rotation angle (degrees) 99.54739018  
Shift along axis 1001.94611437  
  

> ui mousemode right select

> select clear

> hide #5 models

> show #46 models

> show #47 models

> show #48 models

> show #49 models

> show #5 models

> color #5 #fa807297

> color #5 #fa8072a8

> color #5 #011993ff

> color #5 black

> color #5 #000000a5

> color #5 #00000073

> show #5,46-49 atoms

> style #5,46-49 sphere

Changed 52254 atom styles  

> hide #5,46-49 atoms

> select add #5

26127 atoms, 26409 bonds, 1743 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> style sel sphere

Changed 26127 atom styles  

> show sel surfaces

> hide sel atoms

> color #5 transparent

> color #5 #0000003e

> hide #!5 models

> select subtract #5

3 models selected  
Drag select of 14 cryosparc_P310_J320_002_volume_map.mrc  

> select #14

4 models selected  

> select clear

> ui mousemode right zoom

> save "/Users/shj152/OneDrive - University of
> Copenhagen/PhD/AtlasPaper/docs/fig/bas54_tail_fiber_TC8png.png" width 4200
> height 3186 supersample 4

> show #!10 models

> save "/Users/shj152/OneDrive - University of
> Copenhagen/PhD/AtlasPaper/docs/fig/bas54_tail_fiber_TC8png.png" width 4200
> height 3186 supersample 4

> graphics silhouettes false

> graphics silhouettes true

> graphics silhouettes true width 10 depthJump 10

> graphics silhouettes true width 10 depthJump 1

> graphics silhouettes true width 10 depthJump 0

> graphics silhouettes true width 10 depthJump 100

> graphics silhouettes true width 10 depthJump 10000

> graphics silhouettes true width 10

> graphics silhouettes true width 100

> graphics silhouettes true width 100000


===== 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 Metal - 88.1
OpenGL renderer: Apple M1 Max
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: MacBookPro18,2
      Model Number: Z14V0004GDK/A
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 13 days, 3 hours, 50 minutes

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 32
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.2.2
    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
    Send2Trash: 1.8.3
    SEQCROW: 1.8.8
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by pett, 13 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in event loop

comment:2 by pett, 13 months ago

Resolution: → can't reproduce
Status: accepted → closed
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