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Opened 2 years ago
Closed 2 years ago
#9474 closed defect (nonchimerax)
Graphics crash, macOS 13.4.1, Intel Iris Plus Graphics 640
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x000070001dcd0000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001cccd000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001bcca000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000070001acc7000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700019cc4000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700018cc1000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x0000700017cbe000 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007ff84877d640 (most recent call first):
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2720 in draw_elements
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1723 in draw
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 824 in _draw_geometry
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 759 in draw_self
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 752 in draw
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1539 in _draw_multiple
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1526 in draw_opaque
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 235 in _draw_scene
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 165 in draw
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 276 in render
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/sideview/tool.py", line 112 in _redraw
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 89 in draw_new_frame
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 870 in init
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1021 in
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/nv/232zcsr5453dq263cr0xq2100000gq/T/AppTranslocation/D1196D39-FF8C-4D44-A909-1A36D7AE6618/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 197 in _run_module_as_main
{"app_name":"ChimeraX","timestamp":"2023-07-20 09:28:11.00 -0400","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.4.1 (22F82)","roots_installed":0,"name":"ChimeraX","incident_id":"E05885C7-0E91-4140-9932-2AC407E4CCC8"}
{
"uptime" : 160000,
"procRole" : "Background",
"version" : 2,
"userID" : 503,
"deployVersion" : 210,
"modelCode" : "MacBookPro14,1",
"coalitionID" : 32811,
"osVersion" : {
"train" : "macOS 13.4.1",
"build" : "22F82",
"releaseType" : "User"
},
"captureTime" : "2023-07-20 09:27:45.4235 -0400",
"incident" : "E05885C7-0E91-4140-9932-2AC407E4CCC8",
"pid" : 23269,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-07-20 01:41:51.6950 -0400",
"procStartAbsTime" : 156507323778404,
"procExitAbsTime" : 168917160894318,
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"CB49005B-D574-5213-B3A3-884CE0A65E90","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "08F6D46F-C8B5-6AD8-FF9F-8F5FDF70CB7E",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 640,
"sleepWakeUUID" : "03D52FED-E693-44DC-9611-E04A68FFDFA6",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000000, 0x0000000000000000","rawCodes":[0,0],"type":"EXC_CRASH","signal":"SIGABRT"},
"asi" : {"libsystem_c.dylib":["abort() called"]},
"asiSignatures" : ["Graphics hardware encountered an error and was reset: 0x00000011\n"],
"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},
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===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-400_Atf7IP501-900/ranked_0.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-400_Atf7IP501-900/ranked_1.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-400_Atf7IP501-900/ranked_2.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-400_Atf7IP501-900/ranked_3.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-400_Atf7IP501-900/ranked_4.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_3.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_4.pdb #5
---
Chain | Description
A | No description available
B | No description available
> hide #2 models
> hide #3 models
> hide #4 models
> hide #5 models
> show #5 models
> show #4 models
> show #3 models
> show #2 models
> color bfactor
62490 atoms, 3995 residues, atom bfactor range 20 to 97.8
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> ui mousemode right select
Drag select of 12 residues
> select up
514 atoms, 521 bonds, 34 residues, 1 model selected
> select down
192 atoms, 12 residues, 1 model selected
> select add #1/B:155
202 atoms, 9 bonds, 13 residues, 1 model selected
> select add #1/A:47
217 atoms, 23 bonds, 14 residues, 1 model selected
> select up
1198 atoms, 1208 bonds, 74 residues, 1 model selected
> select up
12498 atoms, 12617 bonds, 799 residues, 1 model selected
> select down
1198 atoms, 1208 bonds, 74 residues, 1 model selected
> select add #1/A:61
1213 atoms, 1222 bonds, 75 residues, 1 model selected
> select up
1448 atoms, 1457 bonds, 89 residues, 1 model selected
> select add #1/B:122
1467 atoms, 1475 bonds, 90 residues, 1 model selected
> select add #1/B:106
1489 atoms, 1496 bonds, 91 residues, 1 model selected
> select add #1/B:88
1511 atoms, 1517 bonds, 92 residues, 1 model selected
> select up
2166 atoms, 2177 bonds, 132 residues, 1 model selected
> select clear
Drag select of 6 residues
Drag select of 8 residues
Drag select of 12 residues
> select up
1025 atoms, 1034 bonds, 64 residues, 1 model selected
> select down
332 atoms, 20 residues, 1 model selected
> select add #1/A:74
342 atoms, 9 bonds, 21 residues, 1 model selected
> select add #1/A:40
359 atoms, 26 bonds, 22 residues, 1 model selected
> select add #1/A:21
369 atoms, 35 bonds, 23 residues, 1 model selected
> select add #1/B:87
379 atoms, 44 bonds, 24 residues, 1 model selected
> select add #1/B:109
389 atoms, 53 bonds, 25 residues, 1 model selected
> select up
2328 atoms, 2339 bonds, 146 residues, 1 model selected
> select down
389 atoms, 53 bonds, 25 residues, 1 model selected
Drag select of 10 residues
> select clear
Drag select of 28 residues
> select clear
> ui mousemode right translate
> ui mousemode right select
Drag select of 2 residues
> select up
68 atoms, 67 bonds, 3 residues, 1 model selected
> select up
6144 atoms, 6204 bonds, 400 residues, 1 model selected
> select down
68 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/B:144
78 atoms, 76 bonds, 4 residues, 1 model selected
> select up
508 atoms, 509 bonds, 29 residues, 1 model selected
> select add #1/B:128
530 atoms, 530 bonds, 30 residues, 1 model selected
> select up
752 atoms, 753 bonds, 43 residues, 1 model selected
> select add #1/B:132
766 atoms, 766 bonds, 44 residues, 1 model selected
> select up
799 atoms, 799 bonds, 46 residues, 1 model selected
> select up
6144 atoms, 6204 bonds, 400 residues, 1 model selected
> select down
799 atoms, 799 bonds, 46 residues, 1 model selected
> select add #1/B:134
823 atoms, 822 bonds, 47 residues, 1 model selected
> select add #1/B:130
838 atoms, 836 bonds, 48 residues, 1 model selected
> select up
857 atoms, 859 bonds, 49 residues, 1 model selected
> select clear
Drag select of 13 residues
> select up
545 atoms, 546 bonds, 32 residues, 1 model selected
> select #1/B:163
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
68 atoms, 67 bonds, 3 residues, 1 model selected
> select up
6144 atoms, 6204 bonds, 400 residues, 1 model selected
> select down
68 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/B:145
90 atoms, 88 bonds, 4 residues, 1 model selected
> select add #1/B:130
105 atoms, 102 bonds, 5 residues, 1 model selected
> select up
542 atoms, 542 bonds, 31 residues, 1 model selected
> select add #1/B:132
556 atoms, 555 bonds, 32 residues, 1 model selected
> select up
589 atoms, 589 bonds, 34 residues, 1 model selected
> select add #1/B:134
613 atoms, 612 bonds, 35 residues, 1 model selected
> select clear
> select add #1/B:163
24 atoms, 23 bonds, 1 residue, 1 model selected
> select up
68 atoms, 67 bonds, 3 residues, 1 model selected
> select up
6144 atoms, 6204 bonds, 400 residues, 1 model selected
> select down
68 atoms, 67 bonds, 3 residues, 1 model selected
> select add #1/B:141
83 atoms, 81 bonds, 4 residues, 1 model selected
> select up
508 atoms, 509 bonds, 29 residues, 1 model selected
> select add #1/B:125
532 atoms, 532 bonds, 30 residues, 1 model selected
> select up
752 atoms, 753 bonds, 43 residues, 1 model selected
> select add #1/B:130
767 atoms, 767 bonds, 44 residues, 1 model selected
> select up
786 atoms, 787 bonds, 45 residues, 1 model selected
> select add #1/B:132
800 atoms, 800 bonds, 46 residues, 1 model selected
> select up
833 atoms, 834 bonds, 48 residues, 1 model selected
> select add #1/B:134
857 atoms, 857 bonds, 49 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select add #1/B:102
876 atoms, 875 bonds, 50 residues, 1 model selected
> select up
1331 atoms, 1335 bonds, 78 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right select
> select add #1/B:80
1346 atoms, 1349 bonds, 79 residues, 1 model selected
> select up
1421 atoms, 1425 bonds, 83 residues, 1 model selected
> select add #1/B:85
1440 atoms, 1443 bonds, 84 residues, 1 model selected
> ui mousemode right translate
> ui mousemode right rotate
> ui mousemode right select
> select add #1/A:106
1464 atoms, 1466 bonds, 85 residues, 1 model selected
> select add #1/A:104
1481 atoms, 1482 bonds, 86 residues, 1 model selected
> select up
2026 atoms, 2033 bonds, 125 residues, 1 model selected
> ui mousemode right rotate
> select down
1481 atoms, 1482 bonds, 86 residues, 1 model selected
> ui mousemode right select
> select add #1/A:105
1502 atoms, 1503 bonds, 87 residues, 1 model selected
> select add #1/A:102
1509 atoms, 1509 bonds, 88 residues, 1 model selected
> select add #1/A:103
1528 atoms, 1527 bonds, 89 residues, 1 model selected
> select add #1/A:100
1550 atoms, 1548 bonds, 90 residues, 1 model selected
> select up
2099 atoms, 2107 bonds, 129 residues, 1 model selected
> select down
1550 atoms, 1548 bonds, 90 residues, 1 model selected
> select add #1/A:101
1569 atoms, 1566 bonds, 91 residues, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> select add #1/A:85
1593 atoms, 1589 bonds, 92 residues, 1 model selected
> select add #1/A:78
1610 atoms, 1605 bonds, 93 residues, 1 model selected
> select add #1/A:70
1625 atoms, 1619 bonds, 94 residues, 1 model selected
> select up
2466 atoms, 2475 bonds, 154 residues, 1 model selected
> select down
1625 atoms, 1619 bonds, 94 residues, 1 model selected
> select add #1/A:94
1641 atoms, 1634 bonds, 95 residues, 1 model selected
> select up
2523 atoms, 2532 bonds, 157 residues, 1 model selected
> select subtract #1/A:110
2512 atoms, 2520 bonds, 156 residues, 1 model selected
> select subtract #1/A:112
2500 atoms, 2507 bonds, 155 residues, 1 model selected
> select subtract #1/A:111
2485 atoms, 2493 bonds, 154 residues, 1 model selected
> select subtract #1/A:109
2474 atoms, 2482 bonds, 153 residues, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> select subtract #1/A:132
2463 atoms, 2470 bonds, 152 residues, 1 model selected
> select subtract #1/A:131
2444 atoms, 2451 bonds, 151 residues, 1 model selected
> select subtract #1/A:121
2425 atoms, 2431 bonds, 150 residues, 1 model selected
> select subtract #1/A:123
2406 atoms, 2411 bonds, 149 residues, 1 model selected
> select subtract #1/A:124
2392 atoms, 2396 bonds, 148 residues, 1 model selected
> select subtract #1/A:125
2380 atoms, 2384 bonds, 147 residues, 1 model selected
> select subtract #1/A:127
2368 atoms, 2371 bonds, 146 residues, 1 model selected
> select subtract #1/A:128
2356 atoms, 2359 bonds, 145 residues, 1 model selected
> select subtract #1/A:129
2344 atoms, 2347 bonds, 144 residues, 1 model selected
> select subtract #1/A:130
2328 atoms, 2332 bonds, 143 residues, 1 model selected
> select subtract #1/A:134
2316 atoms, 2319 bonds, 142 residues, 1 model selected
> select subtract #1/A:137
2304 atoms, 2306 bonds, 141 residues, 1 model selected
> select subtract #1/A:135
2293 atoms, 2295 bonds, 140 residues, 1 model selected
> select subtract #1/A:139
2286 atoms, 2287 bonds, 139 residues, 1 model selected
> select subtract #1/A:140
2275 atoms, 2276 bonds, 138 residues, 1 model selected
> select subtract #1/A:138
2265 atoms, 2267 bonds, 137 residues, 1 model selected
> select subtract #1/A:141
2241 atoms, 2243 bonds, 136 residues, 1 model selected
> select subtract #1/A:142
2227 atoms, 2230 bonds, 135 residues, 1 model selected
> select subtract #1/A:133
2208 atoms, 2212 bonds, 134 residues, 1 model selected
> select subtract #1/A:136
2201 atoms, 2206 bonds, 133 residues, 1 model selected
> select subtract #1/A:126
2186 atoms, 2192 bonds, 132 residues, 1 model selected
> select subtract #1/A:122
2171 atoms, 2178 bonds, 131 residues, 1 model selected
> select subtract #1/A:120
2152 atoms, 2159 bonds, 130 residues, 1 model selected
> select subtract #1/A:119
2137 atoms, 2144 bonds, 129 residues, 1 model selected
> select subtract #1/A:118
2123 atoms, 2130 bonds, 128 residues, 1 model selected
> ui mousemode right rotate
> ui mousemode right select
> select subtract #1/A:117
2109 atoms, 2115 bonds, 127 residues, 1 model selected
> select subtract #1/A:116
2085 atoms, 2091 bonds, 126 residues, 1 model selected
> select subtract #1/A:114
2074 atoms, 2079 bonds, 125 residues, 1 model selected
> select add #1/A:161
2086 atoms, 2090 bonds, 126 residues, 1 model selected
> select subtract #1/A:161
2074 atoms, 2079 bonds, 125 residues, 1 model selected
> select subtract #1/A:115
2063 atoms, 2069 bonds, 124 residues, 1 model selected
> ui mousemode right zoom
> ui mousemode right select
> select add #1/A:115
2074 atoms, 2079 bonds, 125 residues, 1 model selected
> select add #1/A:114
2085 atoms, 2089 bonds, 126 residues, 1 model selected
> select add #1/A:116
2109 atoms, 2112 bonds, 127 residues, 1 model selected
> select add #1/A:193
2121 atoms, 2123 bonds, 128 residues, 1 model selected
> select clear
Drag select of 25 residues
> select add #1
12498 atoms, 12617 bonds, 799 residues, 1 model selected
> select subtract #1
Nothing selected
Alignment identifier is 1
Alignment identifier is 2
> select
> #1/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #2/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #3/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #4/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #5/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
14205 atoms, 14255 bonds, 875 residues, 5 models selected
> select add #1
23862 atoms, 24021 bonds, 1499 residues, 5 models selected
> select add #2
33519 atoms, 33787 bonds, 2123 residues, 5 models selected
> select subtract #2
21021 atoms, 21170 bonds, 1324 residues, 4 models selected
> select subtract #1
8523 atoms, 8553 bonds, 525 residues, 3 models selected
> select add #3
18180 atoms, 18319 bonds, 1149 residues, 3 models selected
> select subtract #3
5682 atoms, 5702 bonds, 350 residues, 2 models selected
> select add #5
15339 atoms, 15468 bonds, 974 residues, 2 models selected
> select add #4
24996 atoms, 25234 bonds, 1598 residues, 2 models selected
> select subtract #4
12498 atoms, 12617 bonds, 799 residues, 1 model selected
> select subtract #5
Nothing selected
> select #1/A:2 #2/A:2 #3/A:2 #4/A:2 #5/A:2
95 atoms, 90 bonds, 5 residues, 5 models selected
> select #1/A:2-147 #2/A:2-147 #3/A:2-147 #4/A:2-147 #5/A:2-147
11175 atoms, 11235 bonds, 730 residues, 5 models selected
1 [ID: 1] region 5 chains [2-147] RMSD: 54.853
> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1
65 atoms, 60 bonds, 5 residues, 5 models selected
> select #1/A:1-143 #2/A:1-143 #3/A:1-143 #4/A:1-143 #5/A:1-143
10875 atoms, 10935 bonds, 715 residues, 5 models selected
1 [ID: 1] region 5 chains [1-143] RMSD: 55.026
> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1
65 atoms, 60 bonds, 5 residues, 5 models selected
> select #1/A:1-123 #2/A:1-123 #3/A:1-123 #4/A:1-123 #5/A:1-123
9555 atoms, 9605 bonds, 615 residues, 5 models selected
1 [ID: 1] region 5 chains [1-123] RMSD: 56.917
> select #1/A:122-123 #2/A:122-123 #3/A:122-123 #4/A:122-123 #5/A:122-123
170 atoms, 165 bonds, 10 residues, 5 models selected
> select #1/A:117-123 #2/A:117-123 #3/A:117-123 #4/A:117-123 #5/A:117-123
575 atoms, 575 bonds, 35 residues, 5 models selected
1 [ID: 1] region 5 chains [117-123] RMSD: 42.048
> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1
65 atoms, 60 bonds, 5 residues, 5 models selected
> select #1/A:1-122 #2/A:1-122 #3/A:1-122 #4/A:1-122 #5/A:1-122
9460 atoms, 9510 bonds, 610 residues, 5 models selected
1 [ID: 1] region 5 chains [1-122] RMSD: 57.014
> select
> #1/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #2/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #3/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #4/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
> #5/B:19-28,47-165,195-207,210-213,222-224,228-231,240-246,255-258,352-354,389-391,393-397
14205 atoms, 14255 bonds, 875 residues, 5 models selected
> select #1/B:44 #2/B:44 #3/B:44 #4/B:44 #5/B:44
120 atoms, 115 bonds, 5 residues, 5 models selected
> select #1/B:44-223 #2/B:44-223 #3/B:44-223 #4/B:44-223 #5/B:44-223
14745 atoms, 14850 bonds, 900 residues, 5 models selected
2 [ID: 2] region 5 chains [44-223] RMSD: 78.523
> select clear
> select #1/A:1-2 #2/A:1-2 #3/A:1-2 #4/A:1-2 #5/A:1-2
160 atoms, 155 bonds, 10 residues, 5 models selected
> select #1/A:1-122 #2/A:1-122 #3/A:1-122 #4/A:1-122 #5/A:1-122
9460 atoms, 9510 bonds, 610 residues, 5 models selected
1 [ID: 1] region 5 chains [1-122] RMSD: 57.014
> select #1/B:44-224 #2/B:44-224 #3/B:44-224 #4/B:44-224 #5/B:44-224
14815 atoms, 14920 bonds, 905 residues, 5 models selected
2 [ID: 2] region 5 chains [44-223] + 1 other block RMSD: 78.479
> select clear
> select #1/A:1 #2/A:1 #3/A:1 #4/A:1 #5/A:1
65 atoms, 60 bonds, 5 residues, 5 models selected
> select #1/A:1-122 #2/A:1-122 #3/A:1-122 #4/A:1-122 #5/A:1-122
9460 atoms, 9510 bonds, 610 residues, 5 models selected
1 [ID: 1] region 5 chains [1-122] RMSD: 57.014
> ui mousemode right translate
> select #1/B:44 #2/B:44 #3/B:44 #4/B:44 #5/B:44
120 atoms, 115 bonds, 5 residues, 5 models selected
> select #1/B:44-224 #2/B:44-224 #3/B:44-224 #4/B:44-224 #5/B:44-224
14815 atoms, 14920 bonds, 905 residues, 5 models selected
2 [ID: 2] region 5 chains [44-224] RMSD: 78.434
> ui mousemode right zoom
> ui mousemode right translate
> select #1/B:55 #2/B:55 #3/B:55 #4/B:55 #5/B:55
110 atoms, 105 bonds, 5 residues, 5 models selected
> select #1/B:55-112 #2/B:55-112 #3/B:55-112 #4/B:55-112 #5/B:55-112
4920 atoms, 4940 bonds, 290 residues, 5 models selected
2 [ID: 2] region 5 chains [55-112] RMSD: 103.419
> select #1/B:55 #2/B:55 #3/B:55 #4/B:55 #5/B:55
110 atoms, 105 bonds, 5 residues, 5 models selected
> select #1/B:49-55 #2/B:49-55 #3/B:49-55 #4/B:49-55 #5/B:49-55
650 atoms, 650 bonds, 35 residues, 5 models selected
2 [ID: 2] region 5 chains [49-55] RMSD: 132.966
> select #1/B:47 #2/B:47 #3/B:47 #4/B:47 #5/B:47
75 atoms, 70 bonds, 5 residues, 5 models selected
> select #1/B:47-206 #2/B:47-206 #3/B:47-206 #4/B:47-206 #5/B:47-206
13320 atoms, 13400 bonds, 800 residues, 5 models selected
2 [ID: 2] region 5 chains [47-206] RMSD: 79.698
> select #1/B:55 #2/B:55 #3/B:55 #4/B:55 #5/B:55
110 atoms, 105 bonds, 5 residues, 5 models selected
> select #1/B:55-153 #2/B:55-153 #3/B:55-153 #4/B:55-153 #5/B:55-153
8480 atoms, 8515 bonds, 495 residues, 5 models selected
2 [ID: 2] region 5 chains [55-153] RMSD: 83.369
> select #1/B:64 #2/B:64 #3/B:64 #4/B:64 #5/B:64
70 atoms, 65 bonds, 5 residues, 5 models selected
> select #1/B:64-156 #2/B:64-156 #3/B:64-156 #4/B:64-156 #5/B:64-156
7925 atoms, 7960 bonds, 465 residues, 5 models selected
2 [ID: 2] region 5 chains [64-156] RMSD: 74.663
> select #1/B:69 #2/B:69 #3/B:69 #4/B:69 #5/B:69
120 atoms, 115 bonds, 5 residues, 5 models selected
> select #1/B:69-208 #2/B:69-208 #3/B:69-208 #4/B:69-208 #5/B:69-208
11595 atoms, 11670 bonds, 700 residues, 5 models selected
2 [ID: 2] region 5 chains [69-208] RMSD: 66.309
> select #1/B:69-70 #2/B:69-70 #3/B:69-70 #4/B:69-70 #5/B:69-70
240 atoms, 235 bonds, 10 residues, 5 models selected
> select #1/B:69-71 #2/B:69-71 #3/B:69-71 #4/B:69-71 #5/B:69-71
360 atoms, 355 bonds, 15 residues, 5 models selected
2 [ID: 2] region 5 chains [69-71] RMSD: 124.640
> select #1/B:69-71 #2/B:69-71 #3/B:69-71 #4/B:69-71 #5/B:69-71
360 atoms, 355 bonds, 15 residues, 5 models selected
2 [ID: 2] region 5 chains [69-71] RMSD: 124.640
> select #1/B:82 #2/B:82 #3/B:82 #4/B:82 #5/B:82
85 atoms, 80 bonds, 5 residues, 5 models selected
> select #1/B:82-172 #2/B:82-172 #3/B:82-172 #4/B:82-172 #5/B:82-172
7700 atoms, 7750 bonds, 455 residues, 5 models selected
2 [ID: 2] region 5 chains [82-172] RMSD: 61.660
> close #2
> close
> open
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-194_Atf7IP544-677/ranked_0.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-194_Atf7IP544-677/ranked_1.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-194_Atf7IP544-677/ranked_2.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-194_Atf7IP544-677/ranked_3.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-194_Atf7IP544-677/ranked_4.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_3.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_4.pdb #5
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #2-5 to #1
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 ranked_0.pdb, chain A (#1) with ranked_1.pdb, chain A (#2),
sequence alignment score = 960.3
RMSD between 112 pruned atom pairs is 0.489 angstroms; (across all 191 pairs:
29.564)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_2.pdb, chain A (#3),
sequence alignment score = 897.9
RMSD between 94 pruned atom pairs is 0.560 angstroms; (across all 191 pairs:
25.839)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_3.pdb, chain A (#4),
sequence alignment score = 905.7
RMSD between 94 pruned atom pairs is 0.587 angstroms; (across all 191 pairs:
11.990)
Matchmaker ranked_0.pdb, chain A (#1) with ranked_4.pdb, chain A (#5),
sequence alignment score = 951.3
RMSD between 110 pruned atom pairs is 0.604 angstroms; (across all 191 pairs:
28.007)
> color bfactor
25956 atoms, 1625 residues, atom bfactor range 28.9 to 97.3
> color bychain
> color bfactor
25956 atoms, 1625 residues, atom bfactor range 28.9 to 97.3
> ui mousemode right zoom
> close
> open
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/ranked_0.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/ranked_1.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/ranked_2.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/ranked_3.pdb
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/ranked_4.pdb
Chain information for ranked_0.pdb #1
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_1.pdb #2
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_2.pdb #3
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_3.pdb #4
---
Chain | Description
A | No description available
B | No description available
Chain information for ranked_4.pdb #5
---
Chain | Description
A | No description available
B | No description available
> ui tool show Matchmaker
> matchmaker #2-5 to #1
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 ranked_0.pdb, chain B (#1) with ranked_1.pdb, chain B (#2),
sequence alignment score = 672.1
RMSD between 106 pruned atom pairs is 0.841 angstroms; (across all 134 pairs:
6.205)
Matchmaker ranked_0.pdb, chain B (#1) with ranked_2.pdb, chain B (#3),
sequence alignment score = 672.1
RMSD between 109 pruned atom pairs is 0.947 angstroms; (across all 134 pairs:
7.154)
Matchmaker ranked_0.pdb, chain B (#1) with ranked_3.pdb, chain B (#4),
sequence alignment score = 672.1
RMSD between 110 pruned atom pairs is 0.597 angstroms; (across all 134 pairs:
7.496)
Matchmaker ranked_0.pdb, chain B (#1) with ranked_4.pdb, chain B (#5),
sequence alignment score = 708.7
RMSD between 100 pruned atom pairs is 0.881 angstroms; (across all 134 pairs:
2.490)
> color bfactor
20628 atoms, 1270 residues, atom bfactor range 39 to 97.9
> color bychain
> color bfactor
20628 atoms, 1270 residues, atom bfactor range 39 to 97.9
> set bgColor white
> lighting soft
> lighting simple
> undo
> color bfactor
20628 atoms, 1270 residues, atom bfactor range 39 to 97.9
> set bgColor white
> view
> ui tool show "Side View"
> view
> ui tool show "Side View"
> set bgColor white
No map chosen to save
> save /Users/Leena.Kariapper/Desktop/image1.png supersample 3
> save /Users/Leena.Kariapper/Desktop/image2.png supersample 3
> open
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-400_Atf7IP501-900.fasta
Sequence 'sequence_2' differs in length from preceding sequences, and it is
therefore impossible to open these sequences as an alignment. If you want to
open the sequences individually, specify 'false' as the value of the
'alignment' keyword in the 'open' command.
> ui tool show "AlphaFold Error Plot"
Must choose path to predicted aligned file
> alphafold pae #1 file
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
File
/Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
does not contain AlphaFold predicted aligned error (PAE) data. The AlphaFold
"monomer" preset does not compute PAE. Run AlphaFold with the "monomer_ptm" or
"multimer" presets to get PAE values.
> alphafold pae #1 file
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
File
/Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
does not contain AlphaFold predicted aligned error (PAE) data. The AlphaFold
"monomer" preset does not compute PAE. Run AlphaFold with the "monomer_ptm" or
"multimer" presets to get PAE values.
> alphafold pae #1 file
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
File
/Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
does not contain AlphaFold predicted aligned error (PAE) data. The AlphaFold
"monomer" preset does not compute PAE. Run AlphaFold with the "monomer_ptm" or
"multimer" presets to get PAE values.
> alphafold pae #1 file
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
File
/Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/features.pkl
does not contain AlphaFold predicted aligned error (PAE) data. The AlphaFold
"monomer" preset does not compute PAE. Run AlphaFold with the "monomer_ptm" or
"multimer" presets to get PAE values.
> select add #1
4126 atoms, 4152 bonds, 254 residues, 1 model selected
> select add #2
8252 atoms, 8304 bonds, 508 residues, 2 models selected
> select add #3
12378 atoms, 12456 bonds, 762 residues, 3 models selected
> select add #4
16504 atoms, 16608 bonds, 1016 residues, 4 models selected
> select add #5
20628 atoms, 20758 bonds, 1270 residues, 5 models selected
> ui tool show "AlphaFold Error Plot"
Must choose path to predicted aligned file
> alphafold pae #1 file
> /Volumes/projects/worden/Leena/AlphaFold/Human/Setdb1_2-122_Atf7IP544-677/result_model_1_multimer.pkl
> color bfactor #1 palette alphafold
4126 atoms, 254 residues, atom bfactor range 43.7 to 97.9
> select subtract #5
16504 atoms, 16608 bonds, 1016 residues, 4 models selected
> select subtract #4
12378 atoms, 12456 bonds, 762 residues, 3 models selected
> select subtract #3
8252 atoms, 8304 bonds, 508 residues, 2 models selected
> select subtract #2
4126 atoms, 4152 bonds, 254 residues, 1 model selected
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> alphafold pae #1 colorDomains true
> color bfactor #1 palette alphafold
4126 atoms, 254 residues, atom bfactor range 43.7 to 97.9
> color bfactor sel
4126 atoms, 254 residues, atom bfactor range 43.7 to 97.9
> show #2 models
> show #3 models
> show #4 models
> show #5 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 INTEL-20.6.1
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro14,1
Processor Name: Dual-Core Intel Core i5
Processor Speed: 2.3 GHz
Number of Processors: 1
Total Number of Cores: 2
L2 Cache (per Core): 256 KB
L3 Cache: 4 MB
Hyper-Threading Technology: Enabled
Memory: 8 GB
System Firmware Version: 512.0.0.0.0
OS Loader Version: 577~170
SMC Version (system): 2.43f11
Software:
System Software Overview:
System Version: macOS 13.4.1 (22F82)
Kernel Version: Darwin 22.5.0
Time since boot: 17 days, 10 hours, 9 minutes
Graphics/Displays:
Intel Iris Plus Graphics 640:
Chipset Model: Intel Iris Plus Graphics 640
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x5926
Revision ID: 0x0006
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.3
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.10.8
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
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
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
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
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Graphics hardware encountered an error and was reset |
comment:2 by , 2 years ago
| Resolution: | → nonchimerax |
|---|---|
| Status: | assigned → closed |
| Summary: | Graphics hardware encountered an error and was reset → Graphics crash, macOS 13.4.1, Intel Iris Plus Graphics 640 |
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Apple Intel graphics driver crash.