![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Last modified 2 years ago
#9663 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| 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-13.5-arm64-arm-64bit
ChimeraX Version: 1.7.dev202305160152 (2023-05-16 01:52:41 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error
Thread 0x000000029710b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002960ff000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002950f3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002940e7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002930db000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002920cf000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002910c3000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000002900b7000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028f0ab000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028e09f000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028d093000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028c087000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000028b07b000 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00000001f88c2080 (most recent call first):
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py", line 125 in glBufferSubData
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py", line 2702 in update_buffer_data
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1904 in update_buffers
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1916 in activate_bindings
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 803 in _draw_geometry
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 776 in draw_self
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 769 in draw
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1556 in _draw_multiple
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/drawing.py", line 1543 in draw_opaque
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 247 in _draw_scene
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py", line 177 in draw
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 73 in draw_new_frame
File "/Applications/ChimeraX_Daily.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 "/Applications/ChimeraX_Daily.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_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in
File "/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/Applications/ChimeraX_Daily.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":"2023-08-29 16:27:04.00 -0500","app_version":"1.7.0","slice_uuid":"a5992708-d5b4-36ec-ac0a-e525f6105b56","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.5 (22G74)","roots_installed":0,"name":"ChimeraX","incident_id":"ADF95627-23DF-4DC4-B9B2-FB916777A929"}
{
"uptime" : 560000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro18,1",
"coalitionID" : 71879,
"osVersion" : {
"train" : "macOS 13.5",
"build" : "22G74",
"releaseType" : "User"
},
"captureTime" : "2023-08-29 16:26:53.5649 -0500",
"incident" : "ADF95627-23DF-4DC4-B9B2-FB916777A929",
"pid" : 18713,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-08-28 15:00:28.1598 -0500",
"procStartAbsTime" : 12827957681887,
"procExitAbsTime" : 13503122748654,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"8B194EE4-C40E-5B5C-9783-DC9A8D14938F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "C8325DBF-E4AA-C806-BD0F-A70D9DE3ADB6",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 0,
"wakeTime" : 2975,
"sleepWakeUUID" : "5ABCCC79-B1A8-47BB-BED1-53E21D2EC198",
"sip" : "enabled",
"vmRegionInfo" : "0x1205f8000 is in 0x1205f8000-0x1205fc000; bytes after start: 0 bytes before end: 16383\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n ColorSync 1205d4000-1205d8000 [ 16K] r--\/r-- SM=COW \n GAP OF 0x20000 BYTES\n---> mapped file 1205f8000-1205fc000 [ 16K] r--\/rwx SM=COW ...t_id=bc10b421\n shared memory 1205fc000-120600000 [ 16K] rw-\/rw- SM=SHM ",
"exception" : {"codes":"0x0000000000000002, 0x00000001205f8000","rawCodes":[2,4838096896],"type":"EXC_BAD_ACCESS","signal":"SIGBUS","subtype":"KERN_PROTECTION_FAILURE at 0x00000001205f8000"},
"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":18713},
"vmregioninfo" : "0x1205f8000 is in 0x1205f8000-0x1205fc000; bytes after start: 0 bytes before end: 16383\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n ColorSync 1205d4000-1205d8000 [ 16K] r--\/r-- SM=COW \n GAP OF 0x20000 BYTES\n---> mapped file 1205f8000-1205fc000 [ 16K] r--\/rwx SM=COW ...t_id=bc10b421\n shared memory 1205fc000-120600000 [ 16K] rw-\/rw- SM=SHM ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : [{"triggered":true,"id":11031582,"threadState":{"x":[{"value":0},{"value":0},{"value":1},{"value":6937820588},{"value":4966579224},{"value":4797125652965622844},{"value":4284},{"value":0},{"value":7438232731336512979},{"value":7438232735756531027},{"value":78},{"value":0},{"value":49},{"value":4760175280},{"value":72057602518295905,"symbolLocation":72057594037927937,"symbol":"OBJC_CLASS_$_AGXG13XFamilyBuffer"},{"value":8480367968,"symbolLocation":0,"symbol":"OBJC_CLASS_$_AGXG13XFamilyBuffer"},{"value":328},{"value":8543695776},{"value":0},{"value":10},{"value":8464900224,"symbolLocation":0,"symbol":"_main_thread"},{"value":259},{"value":8464900448,"symbolLocation":224,"symbol":"_main_thread"},{"value":11882453392},{"value":4967441832},{"value":49896144896},{"value":105560811773056},{"value":11882324384},{"value":6131457704}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6937639976},"cpsr":{"value":1073745920},"fp":{"value":4966579024},"sp":{"value":4966578992},"esr":{"value":1442840704,"description":" 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"vmSummary" : "ReadOnly portion of Libraries: Total=1.6G resident=0K(0%) swapped_out_or_unallocated=1.6G(100%)\nWritable regions: Total=58.3G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=58.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 8384K 12 \nCG image 3232K 74 \nColorSync 592K 30 \nCoreAnimation 13.1M 337 \nCoreGraphics 64K 4 \nCoreImage 112K 7 \nCoreServices 624K 2 \nCoreUI image data 4576K 44 \nFoundation 48K 2 \nKernel Alloc Once 32K 1 \nMALLOC 51.2G 1711 \nMALLOC guard page 192K 11 \nMALLOC_MEDIUM (reserved) 336.0M 6 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 96K 5 \nOpenGL GLSL 384K 4 \nSTACK GUARD 784K 49 \nStack 377.7M 50 \nStack Guard 56.0M 1 \nVM_ALLOCATE 6.0G 881 \nVM_ALLOCATE (reserved) 192.0M 2 reserved VM address space (unallocated)\n__AUTH 1844K 370 \n__AUTH_CONST 28.8M 604 \n__CTF 824 1 \n__DATA 20.3M 754 \n__DATA_CONST 39.0M 762 \n__DATA_DIRTY 1973K 229 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 831.3M 157 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 852.2M 782 \ndyld private memory 272K 2 \nmapped file 535.6M 93 \nshared memory 3264K 29 \n=========== ======= ======= \nTOTAL 60.7G 7027 \nTOTAL, minus reserved VM space 59.9G 7027 \n",
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===== Log before crash start =====
UCSF ChimeraX version: 1.7.dev202305160152 (2023-05-16)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/prash_mbp/Dropbox (VU Basic
> Sciences)/Iverson_Prash/Letterhead/MSC-ring.cxs" format session
Opened C34_resampled.mrc as #3.1, grid size 1308,1308,1308, pixel 0.8, shown
at level 0.0806, step 1, values float32
Opened C11_resampled.mrc as #3.2, grid size 1308,1308,1308, pixel 0.8, shown
at level 0.144, step 1, values float32
Opened C34_resampled.mrc zone as #4, grid size 600,602,201, pixel 0.8, shown
at level 0.0806, step 1, values float32
Opened C11_resampled.mrc zone as #5, grid size 312,311,164, pixel 0.8, shown
at level 0.144, step 1, values float32
opened ChimeraX session
> ui tool show "Side View"
> open 6ySF
6ysf title:
Structure of the flagellar MotAB stator complex from Clostridium sporogenes
[more info...]
Chain information for 6ysf #6
---
Chain | Description | UniProt
A B | Chemotaxis motB protein | A0A1V9IL35_CLOSG 1-251
C D E F G | Chemotaxis MotA protein | A0A2X3BQ48_CLOSG 1-270
> view
> hide #!3 models
> select add #6
10220 atoms, 10387 bonds, 1327 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models #6,1,0,0,-1.3467,0,1,0,102,0,0,1,389.38
> view matrix models #6,1,0,0,179.13,0,1,0,341.64,0,0,1,278.85
> view matrix models
> #6,0.93336,0.040912,-0.35659,222.62,0.28894,0.50377,0.81408,268.91,0.21295,-0.86287,0.45838,405.91
> view matrix models
> #6,0.93943,0.010777,-0.34256,223.46,0.29294,0.49356,0.81889,268.98,0.1779,-0.86965,0.46051,410.16
> view matrix models
> #6,0.93501,0.028624,-0.35345,223.35,0.30573,0.4399,0.8444,270.21,0.17965,-0.89759,0.40256,419.42
> view matrix models
> #6,0.93501,0.028624,-0.35345,263.75,0.30573,0.4399,0.8444,283.48,0.17965,-0.89759,0.40256,483.85
> show sel cartoons
> hide sel atoms
> cartoon style width 2.5 thickness 1.2
> cartoon style width 2.5 thickness 2
> cartoon style width 3 thickness 2
> cartoon style width 3 thickness 2.5
> cartoon style width 3 thickness 2
> cartoon style width 4 thickness 2
> cartoon style width 3.5 thickness 2
> view matrix models
> #6,0.9453,-0.065498,-0.31955,268.4,0.3158,0.42916,0.84622,283.27,0.081714,-0.90085,0.42637,492.15
> view matrix models
> #6,0.94311,-0.035598,-0.33057,266.83,0.31272,0.43267,0.84558,283.32,0.11293,-0.90085,0.41918,489.57
> view matrix models
> #6,0.93532,-0.0043271,-0.35379,267.11,0.32811,0.38477,0.86273,284.59,0.13239,-0.923,0.3613,496.24
> view matrix models
> #6,0.93532,-0.0043271,-0.35379,274.8,0.32811,0.38477,0.86273,282.73,0.13239,-0.923,0.3613,503.51
> view matrix models
> #6,0.4104,-0.25599,-0.87524,416.48,0.90585,0.22486,0.35899,293.01,0.10491,-0.94016,0.32418,512.44
> view matrix models
> #6,0.4104,-0.25599,-0.87524,421.58,0.90585,0.22486,0.35899,259.1,0.10491,-0.94016,0.32418,515.05
> select subtract #6
Nothing selected
> select add #6
10220 atoms, 10387 bonds, 1327 residues, 1 model selected
> show sel surfaces
> hide sel cartoons
> color sel bychain
> view matrix models
> #6,0.4104,-0.25599,-0.87524,443.66,0.90585,0.22486,0.35899,452.15,0.10491,-0.94016,0.32418,447.73
> view matrix models
> #6,0.4104,-0.25599,-0.87524,451.99,0.90585,0.22486,0.35899,510.06,0.10491,-0.94016,0.32418,514.37
> view matrix models
> #6,0.41786,-0.2779,-0.86496,452.41,0.89565,0.28562,0.34092,506.58,0.15231,-0.91717,0.36825,501.79
> view matrix models
> #6,0.97166,0.21403,0.10029,235.15,-0.16007,0.28363,0.94548,553.75,0.17391,-0.93474,0.30986,507.64
> view matrix models
> #6,0.97651,0.18597,0.10879,236.73,-0.16511,0.32149,0.93241,551.63,0.13842,-0.92847,0.34464,506.89
> view matrix models
> #6,0.97651,0.18597,0.10879,237.73,-0.16511,0.32149,0.93241,553.28,0.13842,-0.92847,0.34464,507.24
> select subtract #6
7 models selected
> select #1/f/g/m/n/p/q
6030 atoms, 6083 bonds, 910 residues, 1 model selected
> select ~sel
274055 atoms, 276631 bonds, 77 pseudobonds, 40366 residues, 15 models selected
> select subtract #2
209210 atoms, 211126 bonds, 31357 residues, 20 models selected
> select subtract #3
209210 atoms, 211126 bonds, 31357 residues, 13 models selected
> select subtract #4
209210 atoms, 211126 bonds, 31357 residues, 11 models selected
> select subtract #5
209210 atoms, 211126 bonds, 31357 residues, 9 models selected
> select subtract #6
198990 atoms, 200739 bonds, 30030 residues, 8 models selected
> transparency sel 90 target c
> transparency sel 100 target c
> view
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> select subtract #1
Nothing selected
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> graphics silhouettes true width 2 depthJump .1
> graphics silhouettes true width 1.5 depthJump .1
> lighting full
> lighting soft
> lighting simple
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes false
> graphics silhouettes true
> graphics silhouettes true width 1 depthJump .1
> turn x
> turn y
> turn y 10
> turn y -10
> lighting full
> lighting soft
> lighting simple
> turn x
> lighting full
> rainbow #1/g:280-290
> lighting full
> lighting simple
> turn y 1
> lighting full
> ui tool show "Side View"
> view
> view orient
> turn x
> turn y -1
> turn x
> select add #6
10220 atoms, 10387 bonds, 1327 residues, 1 model selected
> transparency (#!6 & sel) 50
> transparency (#!6 & sel) 90
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.97651,0.18597,0.10879,210.71,-0.16511,0.32149,0.93241,525.41,0.13842,-0.92847,0.34464,507.24
> view matrix models
> #6,0.97651,0.18597,0.10879,214.55,-0.16511,0.32149,0.93241,521.91,0.13842,-0.92847,0.34464,507.4
> view matrix models
> #6,0.97651,0.18597,0.10879,213.48,-0.16511,0.32149,0.93241,520.32,0.13842,-0.92847,0.34464,507.43
> view matrix models
> #6,0.85903,0.26797,0.43619,180.47,-0.49622,0.22639,0.83816,576.59,0.12585,-0.93645,0.32745,511.56
> view matrix models
> #6,0.85903,0.26797,0.43619,176.45,-0.49622,0.22639,0.83816,575.45,0.12585,-0.93645,0.32745,511.66
> view
> view orient
> turn x
> transparency (#!6 & sel) 0
> lighting full
> turn y -1
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> lighting simple
> lighting full
> lighting soft
> select subtract #6
7 models selected
> graphics silhouettes false
> graphics silhouettes true
> lighting full
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/overview-torque.png" width 1954
> height 1323 supersample 3
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/closeup-torque.png" width 1954
> height 1323 supersample 3
> lighting soft
> lighting full
> lighting simple
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/overview-torque.png" width 1954
> height 1323 supersample 3 transparentBackground true
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/overview-torque.png" width 1954
> height 1323 supersample 3
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/CCW.cxs"
> close #3
> close #4
> close #5
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/CCW_Vs_CW_Comparison/Just4fun_CW_3AJC.pdb"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly_C-ring]/Figures/RAW
Figures/CCW_Vs_CW_Comparison/Just4fun_CW_3AJC.pdb
---
warnings | Ignored bad PDB record found on line 237
Ignored bad PDB record found on line 3233
Ignored bad PDB record found on line 5321
Ignored bad PDB record found on line 5779
Ignored bad PDB record found on line 6170
1 messages similar to the above omitted
Duplicate atom serial number found: 1
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Duplicate atom serial number found: 235
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451 messages similar to the above omitted
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Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 120953
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
Ignored bad PDB record found on line 123499
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 127493
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
Ignored bad PDB record found on line 130039
Duplicate atom serial number found: 5771
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384 messages similar to the above omitted
Ignored bad PDB record found on line 130430
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 134033
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451 messages similar to the above omitted
Ignored bad PDB record found on line 136579
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 136970
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 140573
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451 messages similar to the above omitted
Ignored bad PDB record found on line 143119
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 147113
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Ignored bad PDB record found on line 149201
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451 messages similar to the above omitted
Ignored bad PDB record found on line 149659
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 150050
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 153653
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451 messages similar to the above omitted
Ignored bad PDB record found on line 156199
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
Ignored bad PDB record found on line 160193
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451 messages similar to the above omitted
Ignored bad PDB record found on line 162739
Duplicate atom serial number found: 5771
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384 messages similar to the above omitted
Ignored bad PDB record found on line 163130
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364 messages similar to the above omitted
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Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
Ignored bad PDB record found on line 169279
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 169670
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364 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
Ignored bad PDB record found on line 175819
Duplicate atom serial number found: 5771
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
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Duplicate atom serial number found: 5774
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
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Duplicate atom serial number found: 5774
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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Duplicate atom serial number found: 1
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229 messages similar to the above omitted
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Duplicate atom serial number found: 239
2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
Ignored bad PDB record found on line 201979
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 202370
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364 messages similar to the above omitted
Ignored bad PDB record found on line 202741
Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 202977
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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2081 messages similar to the above omitted
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451 messages similar to the above omitted
Ignored bad PDB record found on line 215059
Duplicate atom serial number found: 5771
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
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364 messages similar to the above omitted
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Duplicate atom serial number found: 1
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229 messages similar to the above omitted
Ignored bad PDB record found on line 216057
Duplicate atom serial number found: 235
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Duplicate atom serial number found: 239
2989 messages similar to the above omitted
Ignored bad PDB record found on line 219053
Duplicate atom serial number found: 3229
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2081 messages similar to the above omitted
Ignored bad PDB record found on line 221141
Duplicate atom serial number found: 5315
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451 messages similar to the above omitted
Ignored bad PDB record found on line 221599
Duplicate atom serial number found: 5771
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384 messages similar to the above omitted
Ignored bad PDB record found on line 221990
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364 messages similar to the above omitted
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Ignored bad PDB record found on line 222362
Chain information for Just4fun_CW_3AJC.pdb #3
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> select add #3
221952 atoms, 224400 bonds, 30940 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> cartoon style width 3.5 thickness 2
> transparency sel 100 target c
> transparency sel 50 target c
> hide #1 models
> turn x
> select subtract #3
Nothing selected
> select add #3
221952 atoms, 224400 bonds, 30940 residues, 1 model selected
> select add #6
232172 atoms, 234787 bonds, 32267 residues, 4 models selected
> select subtract #3
10220 atoms, 10387 bonds, 1327 residues, 10 models selected
> transparency (#!6 & sel) 80
> turn x
> view matrix models
> #6,0.87115,0.21584,0.44103,180.28,-0.48205,0.20504,0.85181,574.74,0.093428,-0.95466,0.28267,522.03
> ui mousemode right "translate selected models"
> view matrix models
> #6,0.90971,-0.0056227,-0.4152,294.28,0.3797,0.41601,0.8263,461.55,0.16808,-0.90934,0.38058,498.29
> view matrix models
> #6,0.90971,-0.0056227,-0.4152,308.39,0.3797,0.41601,0.8263,444.43,0.16808,-0.90934,0.38058,495.06
> view matrix models
> #6,0.90971,-0.0056227,-0.4152,309.24,0.3797,0.41601,0.8263,445.89,0.16808,-0.90934,0.38058,502.12
> view matrix models
> #6,0.90971,-0.0056227,-0.4152,310.84,0.3797,0.41601,0.8263,446.34,0.16808,-0.90934,0.38058,502.65
> view matrix models
> #6,0.91564,-0.037587,-0.40023,312.05,0.37846,0.41624,0.82675,446.4,0.13552,-0.90848,0.39535,504.48
> view matrix models
> #6,0.90863,-0.00038778,-0.4176,310.65,0.3799,0.41597,0.82622,446.33,0.17339,-0.90938,0.37811,502.34
> view matrix models
> #6,0.90931,-0.0036392,-0.41611,310.78,0.37978,0.41599,0.82627,446.33,0.17009,-0.90936,0.37965,502.51
> view matrix models
> #6,0.82251,-0.087816,-0.56193,344.64,0.54496,0.40445,0.73446,439.77,0.16278,-0.91033,0.38052,503.3
> view matrix models
> #6,0.82251,-0.087816,-0.56193,345.95,0.54496,0.40445,0.73446,439.29,0.16278,-0.91033,0.38052,502.91
> select #3/b/c/h/e/d
6294 atoms, 6367 bonds, 863 residues, 1 model selected
> select ~sel
495743 atoms, 500747 bonds, 77 pseudobonds, 71353 residues, 7 models selected
> select subtract #2
430898 atoms, 435242 bonds, 62344 residues, 12 models selected
> select subtract #1
225878 atoms, 228420 bonds, 31404 residues, 11 models selected
> select subtract #6
215658 atoms, 218033 bonds, 30077 residues, 8 models selected
> transparency sel 100 target c
> select #3/b
2994 atoms, 3033 bonds, 320 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #ed271dff
> select #3/c
2086 atoms, 2123 bonds, 296 residues, 1 model selected
> color sel #ffb60aff
> select #3/h
369 atoms, 368 bonds, 75 residues, 1 model selected
> color sel #b581c5ff
> select #3/e
389 atoms, 388 bonds, 79 residues, 1 model selected
> color sel #dc4166ff
> select #3/d
456 atoms, 455 bonds, 93 residues, 1 model selected
> color sel #8c15b7ff
> select add #3
221952 atoms, 224400 bonds, 30940 residues, 1 model selected
> select subtract #3
Nothing selected
> rainbow #3/b:282-294
> select add #3
221952 atoms, 224400 bonds, 30940 residues, 1 model selected
> select subtract #3
Nothing selected
> select add #6
10220 atoms, 10387 bonds, 1327 residues, 3 models selected
> transparency (#!6 & sel) 0
> select subtract #6
7 models selected
> view
> view orient
> turn x
> turn y -1
> select add #6
10220 atoms, 10387 bonds, 1327 residues, 1 model selected
> view matrix models
> #6,0.82251,-0.087816,-0.56193,345,0.54496,0.40445,0.73446,439.69,0.16278,-0.91033,0.38052,497.41
> select subtract #6
7 models selected
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/CW.cxs"
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/CW-overview-torque.png" width
> 1954 height 1323 supersample 3
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly_C-
> ring]/Figures/RAW Figures/Torque Mechanism/CW.cxs"
> close session
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/EMDB and PDB Upload/C-ring/34-mer C-ring/C34_C-
> ring_RSR158-pdb_extract.cif"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly__C-ring]/EMDB and PDB Upload/C-ring/34-mer
C-ring/C34_C-ring_RSR158-pdb_extract.cif
---
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.
Chain information for C34_C-ring_RSR158-pdb_extract.cif #1
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> select :1744
Nothing selected
> select :174
544 atoms, 510 bonds, 68 residues, 1 model selected
> lighting full
> lighting soft
> select add #1
205020 atoms, 206822 bonds, 30940 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select :174
544 atoms, 510 bonds, 68 residues, 1 model selected
> select :167-324
77690 atoms, 78472 bonds, 10744 residues, 1 model selected
> select
> /AA,AD,AG-B,CC,CF,EB,EE,G-GA,GD,GG,IC,IF,J,KB,KE,MA,MD,MG,OC,OF,QB,QE,SA,SD,SG-T,UC,UF,WB,WE,YA,YD:167-324
41888 atoms, 42126 bonds, 5372 residues, 1 model selected
> select /g:167-324
1232 atoms, 1239 bonds, 158 residues, 1 model selected
> select ~sel
203788 atoms, 205582 bonds, 30782 residues, 1 model selected
> delete sel
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/CW/FliG_167_324.pdb" relModel #1
> close
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/CW/FliG_167_324.pdb"
Chain information for FliG_167_324.pdb #1
---
Chain | Description
G | No description available
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/EMDB and PDB Upload/C-ring/34-mer C-ring/C34_C-
> ring_RSR158-pdb_extract.cif"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly__C-ring]/EMDB and PDB Upload/C-ring/34-mer
C-ring/C34_C-ring_RSR158-pdb_extract.cif
---
warning | Missing or incomplete entity_poly_seq table. Inferred polymer
connectivity.
Chain information for C34_C-ring_RSR158-pdb_extract.cif #2
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> select /g:167-324
2464 atoms, 2478 bonds, 316 residues, 2 models selected
> select subtract #1
1232 atoms, 1239 bonds, 158 residues, 1 model selected
> delete sel
> view
> select add #2
203788 atoms, 205582 bonds, 30782 residues, 1 model selected
> hide sel atoms
> show sel cartoons
> select subtract #2
Nothing selected
> select add #2
203788 atoms, 205582 bonds, 30782 residues, 1 model selected
> select subtract #2
Nothing selected
> open "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Figures/FSM/Just4fun_CW_3AJC.pdb"
Summary of feedback from opening /Users/prash_mbp/Dropbox (VU Basic
Sciences)/[FiguresOnly__C-ring]/Figures/FSM/Just4fun_CW_3AJC.pdb
---
warnings | Ignored bad PDB record found on line 237
Ignored bad PDB record found on line 3233
Ignored bad PDB record found on line 5321
Ignored bad PDB record found on line 5779
Ignored bad PDB record found on line 6170
1 messages similar to the above omitted
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 6777
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2989 messages similar to the above omitted
Ignored bad PDB record found on line 9773
Duplicate atom serial number found: 3229
Duplicate atom serial number found: 3230
Duplicate atom serial number found: 3231
Duplicate atom serial number found: 3232
Duplicate atom serial number found: 3233
2081 messages similar to the above omitted
Ignored bad PDB record found on line 11861
Duplicate atom serial number found: 5315
Duplicate atom serial number found: 5316
Duplicate atom serial number found: 5317
Duplicate atom serial number found: 5318
Duplicate atom serial number found: 5319
451 messages similar to the above omitted
Ignored bad PDB record found on line 12319
Duplicate atom serial number found: 5771
Duplicate atom serial number found: 5772
Duplicate atom serial number found: 5773
Duplicate atom serial number found: 5774
Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 12710
Duplicate atom serial number found: 6160
Duplicate atom serial number found: 6161
Duplicate atom serial number found: 6162
Duplicate atom serial number found: 6163
Duplicate atom serial number found: 6164
364 messages similar to the above omitted
Ignored bad PDB record found on line 13081
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 13317
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2989 messages similar to the above omitted
Ignored bad PDB record found on line 16313
Duplicate atom serial number found: 3229
Duplicate atom serial number found: 3230
Duplicate atom serial number found: 3231
Duplicate atom serial number found: 3232
Duplicate atom serial number found: 3233
2081 messages similar to the above omitted
Ignored bad PDB record found on line 18401
Duplicate atom serial number found: 5315
Duplicate atom serial number found: 5316
Duplicate atom serial number found: 5317
Duplicate atom serial number found: 5318
Duplicate atom serial number found: 5319
451 messages similar to the above omitted
Ignored bad PDB record found on line 18859
Duplicate atom serial number found: 5771
Duplicate atom serial number found: 5772
Duplicate atom serial number found: 5773
Duplicate atom serial number found: 5774
Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 19250
Duplicate atom serial number found: 6160
Duplicate atom serial number found: 6161
Duplicate atom serial number found: 6162
Duplicate atom serial number found: 6163
Duplicate atom serial number found: 6164
364 messages similar to the above omitted
Ignored bad PDB record found on line 19621
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
Duplicate atom serial number found: 5
229 messages similar to the above omitted
Ignored bad PDB record found on line 19857
Duplicate atom serial number found: 235
Duplicate atom serial number found: 236
Duplicate atom serial number found: 237
Duplicate atom serial number found: 238
Duplicate atom serial number found: 239
2989 messages similar to the above omitted
Ignored bad PDB record found on line 22853
Duplicate atom serial number found: 3229
Duplicate atom serial number found: 3230
Duplicate atom serial number found: 3231
Duplicate atom serial number found: 3232
Duplicate atom serial number found: 3233
2081 messages similar to the above omitted
Ignored bad PDB record found on line 24941
Duplicate atom serial number found: 5315
Duplicate atom serial number found: 5316
Duplicate atom serial number found: 5317
Duplicate atom serial number found: 5318
Duplicate atom serial number found: 5319
451 messages similar to the above omitted
Ignored bad PDB record found on line 25399
Duplicate atom serial number found: 5771
Duplicate atom serial number found: 5772
Duplicate atom serial number found: 5773
Duplicate atom serial number found: 5774
Duplicate atom serial number found: 5775
384 messages similar to the above omitted
Ignored bad PDB record found on line 25790
Duplicate atom serial number found: 6160
Duplicate atom serial number found: 6161
Duplicate atom serial number found: 6162
Duplicate atom serial number found: 6163
Duplicate atom serial number found: 6164
364 messages similar to the above omitted
Ignored bad PDB record found on line 26161
Duplicate atom serial number found: 1
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
Duplicate atom serial number found: 4
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451 messages similar to the above omitted
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Duplicate atom serial number found: 5775
384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
Ignored bad PDB record found on line 91190
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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2989 messages similar to the above omitted
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451 messages similar to the above omitted
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Duplicate atom serial number found: 5771
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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229 messages similar to the above omitted
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451 messages similar to the above omitted
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384 messages similar to the above omitted
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364 messages similar to the above omitted
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384 messages similar to the above omitted
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Chain information for Just4fun_CW_3AJC.pdb #3
---
Chain | Description
A BC BF DB DE F FA FD FG HC HF I JB JE LA LD LG NC NF PB PE RA RD RG S TC TF
VB VE XA XD Z ZC ZF | No description available
AA AD AG B CC CF EB EE G GA GD GG IC IF J KB KE MA MD MG OC OF QB QE SA SD SG
T UC UF WB WE YA YD | No description available
AB AE CA CD CG D EC EF GB GE IA ID IG KC KF L MB ME N OA OD OG QC QF SB SE UA
UD UG W WC WF YB YE | No description available
AC AF CB CE EA ED EG GC GF H IB IE KA KD KG MC MF OB OE Q QA QD QG R SC SF UB
UE WA WD WG Y YC YF | No description available
BA BD BG C DC DF FB FE HA HD HG JC JF K LB LE M NA ND NG PC PF RB RE TA TD TG
V VC VF XB XE ZA ZD | No description available
BB BE DA DD DG E FC FF HB HE JA JD JG LC LF NB NE O P PA PD PG RC RF TB TE VA
VD VG X XC XF ZB ZE | No description available
> select add #3
221952 atoms, 224400 bonds, 30940 residues, 1 model selected
> show sel cartoons
> hide sel atoms
> select subtract #3
Nothing selected
> select add #1
1232 atoms, 1239 bonds, 158 residues, 1 model selected
> hide #2 models
> select :174
1156 atoms, 1088 bonds, 136 residues, 3 models selected
> morph
Missing or invalid "structures" argument: empty atom specifier
> morph #1,3/B frames 40
Require at least 2 structures for morph
> morph #1,3 frames 40
models have different number of chains, 1 (Morph - FliG_167_324.pdb #/G) and
204 (Just4fun_CW_3AJC.pdb #3/A,Just4fun_CW_3AJC.pdb #3/AA,Just4fun_CW_3AJC.pdb
#3/AB,Just4fun_CW_3AJC.pdb #3/AC,Just4fun_CW_3AJC.pdb
#3/AD,Just4fun_CW_3AJC.pdb #3/AE,Just4fun_CW_3AJC.pdb
#3/AF,Just4fun_CW_3AJC.pdb #3/AG,Just4fun_CW_3AJC.pdb
#3/B,Just4fun_CW_3AJC.pdb #3/BA,Just4fun_CW_3AJC.pdb
#3/BB,Just4fun_CW_3AJC.pdb #3/BC,Just4fun_CW_3AJC.pdb
#3/BD,Just4fun_CW_3AJC.pdb #3/BE,Just4fun_CW_3AJC.pdb
#3/BF,Just4fun_CW_3AJC.pdb #3/BG,Just4fun_CW_3AJC.pdb
#3/C,Just4fun_CW_3AJC.pdb #3/CA,Just4fun_CW_3AJC.pdb
#3/CB,Just4fun_CW_3AJC.pdb #3/CC,Just4fun_CW_3AJC.pdb
#3/CD,Just4fun_CW_3AJC.pdb #3/CE,Just4fun_CW_3AJC.pdb
#3/CF,Just4fun_CW_3AJC.pdb #3/CG,Just4fun_CW_3AJC.pdb
#3/D,Just4fun_CW_3AJC.pdb #3/DA,Just4fun_CW_3AJC.pdb
#3/DB,Just4fun_CW_3AJC.pdb #3/DC,Just4fun_CW_3AJC.pdb
#3/DD,Just4fun_CW_3AJC.pdb #3/DE,Just4fun_CW_3AJC.pdb
#3/DF,Just4fun_CW_3AJC.pdb #3/DG,Just4fun_CW_3AJC.pdb
#3/E,Just4fun_CW_3AJC.pdb #3/EA,Just4fun_CW_3AJC.pdb
#3/EB,Just4fun_CW_3AJC.pdb #3/EC,Just4fun_CW_3AJC.pdb
#3/ED,Just4fun_CW_3AJC.pdb #3/EE,Just4fun_CW_3AJC.pdb
#3/EF,Just4fun_CW_3AJC.pdb #3/EG,Just4fun_CW_3AJC.pdb
#3/F,Just4fun_CW_3AJC.pdb #3/FA,Just4fun_CW_3AJC.pdb
#3/FB,Just4fun_CW_3AJC.pdb #3/FC,Just4fun_CW_3AJC.pdb
#3/FD,Just4fun_CW_3AJC.pdb #3/FE,Just4fun_CW_3AJC.pdb
#3/FF,Just4fun_CW_3AJC.pdb #3/FG,Just4fun_CW_3AJC.pdb
#3/G,Just4fun_CW_3AJC.pdb #3/GA,Just4fun_CW_3AJC.pdb
#3/GB,Just4fun_CW_3AJC.pdb #3/GC,Just4fun_CW_3AJC.pdb
#3/GD,Just4fun_CW_3AJC.pdb #3/GE,Just4fun_CW_3AJC.pdb
#3/GF,Just4fun_CW_3AJC.pdb #3/GG,Just4fun_CW_3AJC.pdb
#3/H,Just4fun_CW_3AJC.pdb #3/HA,Just4fun_CW_3AJC.pdb
#3/HB,Just4fun_CW_3AJC.pdb #3/HC,Just4fun_CW_3AJC.pdb
#3/HD,Just4fun_CW_3AJC.pdb #3/HE,Just4fun_CW_3AJC.pdb
#3/HF,Just4fun_CW_3AJC.pdb #3/HG,Just4fun_CW_3AJC.pdb
#3/I,Just4fun_CW_3AJC.pdb #3/IA,Just4fun_CW_3AJC.pdb
#3/IB,Just4fun_CW_3AJC.pdb #3/IC,Just4fun_CW_3AJC.pdb
#3/ID,Just4fun_CW_3AJC.pdb #3/IE,Just4fun_CW_3AJC.pdb
#3/IF,Just4fun_CW_3AJC.pdb #3/IG,Just4fun_CW_3AJC.pdb
#3/J,Just4fun_CW_3AJC.pdb #3/JA,Just4fun_CW_3AJC.pdb
#3/JB,Just4fun_CW_3AJC.pdb #3/JC,Just4fun_CW_3AJC.pdb
#3/JD,Just4fun_CW_3AJC.pdb #3/JE,Just4fun_CW_3AJC.pdb
#3/JF,Just4fun_CW_3AJC.pdb #3/JG,Just4fun_CW_3AJC.pdb
#3/K,Just4fun_CW_3AJC.pdb #3/KA,Just4fun_CW_3AJC.pdb
#3/KB,Just4fun_CW_3AJC.pdb #3/KC,Just4fun_CW_3AJC.pdb
#3/KD,Just4fun_CW_3AJC.pdb #3/KE,Just4fun_CW_3AJC.pdb
#3/KF,Just4fun_CW_3AJC.pdb #3/KG,Just4fun_CW_3AJC.pdb
#3/L,Just4fun_CW_3AJC.pdb #3/LA,Just4fun_CW_3AJC.pdb
#3/LB,Just4fun_CW_3AJC.pdb #3/LC,Just4fun_CW_3AJC.pdb
#3/LD,Just4fun_CW_3AJC.pdb #3/LE,Just4fun_CW_3AJC.pdb
#3/LF,Just4fun_CW_3AJC.pdb #3/LG,Just4fun_CW_3AJC.pdb
#3/M,Just4fun_CW_3AJC.pdb #3/MA,Just4fun_CW_3AJC.pdb
#3/MB,Just4fun_CW_3AJC.pdb #3/MC,Just4fun_CW_3AJC.pdb
#3/MD,Just4fun_CW_3AJC.pdb #3/ME,Just4fun_CW_3AJC.pdb
#3/MF,Just4fun_CW_3AJC.pdb #3/MG,Just4fun_CW_3AJC.pdb
#3/N,Just4fun_CW_3AJC.pdb #3/NA,Just4fun_CW_3AJC.pdb
#3/NB,Just4fun_CW_3AJC.pdb #3/NC,Just4fun_CW_3AJC.pdb
#3/ND,Just4fun_CW_3AJC.pdb #3/NE,Just4fun_CW_3AJC.pdb
#3/NF,Just4fun_CW_3AJC.pdb #3/NG,Just4fun_CW_3AJC.pdb
#3/O,Just4fun_CW_3AJC.pdb #3/OA,Just4fun_CW_3AJC.pdb
#3/OB,Just4fun_CW_3AJC.pdb #3/OC,Just4fun_CW_3AJC.pdb
#3/OD,Just4fun_CW_3AJC.pdb #3/OE,Just4fun_CW_3AJC.pdb
#3/OF,Just4fun_CW_3AJC.pdb #3/OG,Just4fun_CW_3AJC.pdb
#3/P,Just4fun_CW_3AJC.pdb #3/PA,Just4fun_CW_3AJC.pdb
#3/PB,Just4fun_CW_3AJC.pdb #3/PC,Just4fun_CW_3AJC.pdb
#3/PD,Just4fun_CW_3AJC.pdb #3/PE,Just4fun_CW_3AJC.pdb
#3/PF,Just4fun_CW_3AJC.pdb #3/PG,Just4fun_CW_3AJC.pdb
#3/Q,Just4fun_CW_3AJC.pdb #3/QA,Just4fun_CW_3AJC.pdb
#3/QB,Just4fun_CW_3AJC.pdb #3/QC,Just4fun_CW_3AJC.pdb
#3/QD,Just4fun_CW_3AJC.pdb #3/QE,Just4fun_CW_3AJC.pdb
#3/QF,Just4fun_CW_3AJC.pdb #3/QG,Just4fun_CW_3AJC.pdb
#3/R,Just4fun_CW_3AJC.pdb #3/RA,Just4fun_CW_3AJC.pdb
#3/RB,Just4fun_CW_3AJC.pdb #3/RC,Just4fun_CW_3AJC.pdb
#3/RD,Just4fun_CW_3AJC.pdb #3/RE,Just4fun_CW_3AJC.pdb
#3/RF,Just4fun_CW_3AJC.pdb #3/RG,Just4fun_CW_3AJC.pdb
#3/S,Just4fun_CW_3AJC.pdb #3/SA,Just4fun_CW_3AJC.pdb
#3/SB,Just4fun_CW_3AJC.pdb #3/SC,Just4fun_CW_3AJC.pdb
#3/SD,Just4fun_CW_3AJC.pdb #3/SE,Just4fun_CW_3AJC.pdb
#3/SF,Just4fun_CW_3AJC.pdb #3/SG,Just4fun_CW_3AJC.pdb
#3/T,Just4fun_CW_3AJC.pdb #3/TA,Just4fun_CW_3AJC.pdb
#3/TB,Just4fun_CW_3AJC.pdb #3/TC,Just4fun_CW_3AJC.pdb
#3/TD,Just4fun_CW_3AJC.pdb #3/TE,Just4fun_CW_3AJC.pdb
#3/TF,Just4fun_CW_3AJC.pdb #3/TG,Just4fun_CW_3AJC.pdb
#3/UA,Just4fun_CW_3AJC.pdb #3/UB,Just4fun_CW_3AJC.pdb
#3/UC,Just4fun_CW_3AJC.pdb #3/UD,Just4fun_CW_3AJC.pdb
#3/UE,Just4fun_CW_3AJC.pdb #3/UF,Just4fun_CW_3AJC.pdb
#3/UG,Just4fun_CW_3AJC.pdb #3/V,Just4fun_CW_3AJC.pdb
#3/VA,Just4fun_CW_3AJC.pdb #3/VB,Just4fun_CW_3AJC.pdb
#3/VC,Just4fun_CW_3AJC.pdb #3/VD,Just4fun_CW_3AJC.pdb
#3/VE,Just4fun_CW_3AJC.pdb #3/VF,Just4fun_CW_3AJC.pdb
#3/VG,Just4fun_CW_3AJC.pdb #3/W,Just4fun_CW_3AJC.pdb
#3/WA,Just4fun_CW_3AJC.pdb #3/WB,Just4fun_CW_3AJC.pdb
#3/WC,Just4fun_CW_3AJC.pdb #3/WD,Just4fun_CW_3AJC.pdb
#3/WE,Just4fun_CW_3AJC.pdb #3/WF,Just4fun_CW_3AJC.pdb
#3/WG,Just4fun_CW_3AJC.pdb #3/X,Just4fun_CW_3AJC.pdb
#3/XA,Just4fun_CW_3AJC.pdb #3/XB,Just4fun_CW_3AJC.pdb
#3/XC,Just4fun_CW_3AJC.pdb #3/XD,Just4fun_CW_3AJC.pdb
#3/XE,Just4fun_CW_3AJC.pdb #3/XF,Just4fun_CW_3AJC.pdb
#3/Y,Just4fun_CW_3AJC.pdb #3/YA,Just4fun_CW_3AJC.pdb
#3/YB,Just4fun_CW_3AJC.pdb #3/YC,Just4fun_CW_3AJC.pdb
#3/YD,Just4fun_CW_3AJC.pdb #3/YE,Just4fun_CW_3AJC.pdb
#3/YF,Just4fun_CW_3AJC.pdb #3/Z,Just4fun_CW_3AJC.pdb
#3/ZA,Just4fun_CW_3AJC.pdb #3/ZB,Just4fun_CW_3AJC.pdb
#3/ZC,Just4fun_CW_3AJC.pdb #3/ZD,Just4fun_CW_3AJC.pdb
#3/ZE,Just4fun_CW_3AJC.pdb #3/ZF)
> select #3/B:167-324
1595 atoms, 1610 bonds, 158 residues, 1 model selected
> select #3/B:172-324
1553 atoms, 1567 bonds, 153 residues, 1 model selected
> select ~sel
425419 atoms, 429653 bonds, 61727 residues, 3 models selected
> select subtract #2
221631 atoms, 224071 bonds, 30945 residues, 2 models selected
> select subtract #1
220399 atoms, 222832 bonds, 30787 residues, 1 model selected
> delete sel
> morph #1,3 frames 40
Computed 41 frame morph #4
> coordset #4 1,41
> show #2 models
> view
> hide #2 models
> show #2 models
> hide #4 models
> show #4 models
> show #3 models
> hide #2 models
> select #3:186-195
79 atoms, 78 bonds, 10 residues, 1 model selected
> delete sel
> morph #1,3 frames 40
Computed 41 frame morph #5
> coordset #5 1,41
> hide #!5 models
> show #!5 models
> show #1 models
> hide #!5 models
> hide #4 models
> show #!3 models
> select add #1
1232 atoms, 1239 bonds, 158 residues, 1 model selected
> show #4 models
> hide #4 models
> show #2 models
> hide #2 models
> show #2 models
> hide #1 models
> show #1 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #2 models
> view matrix models
> #1,0.37268,-0.89798,0.23398,697.83,0.91483,0.31327,-0.25487,249.01,0.15557,0.30904,0.93824,-227.85
> view matrix models
> #1,0.26462,-0.95762,0.11374,840.56,0.94731,0.2802,0.15523,41.657,-0.18052,0.066674,0.98131,32.64
> view matrix models
> #1,0.26462,-0.95762,0.11374,838.71,0.94731,0.2802,0.15523,45.41,-0.18052,0.066674,0.98131,30.46
> view matrix models
> #1,0.23506,-0.93225,0.27504,747.54,0.93325,0.29555,0.20418,14.589,-0.27164,0.20869,0.9395,-7.1679
> view matrix models
> #1,0.23506,-0.93225,0.27504,745.98,0.93325,0.29555,0.20418,12.779,-0.27164,0.20869,0.9395,-5.9059
> ui tool show Matchmaker
> matchmaker #!3 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 FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> matchmaker #!3 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 FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> matchmaker #!3 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 FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> matchmaker #!3 to #1/G pairing bs
Parameters
---
Chain pairing | bs
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> matchmaker #3/B to #1/G pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> matchmaker #3/B to #1/G pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> matchmaker #3/B to #1/G pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker FliG_167_324.pdb, chain G (#1) with Just4fun_CW_3AJC.pdb, chain B
(#3), sequence alignment score = 1195.5
RMSD between 11 pruned atom pairs is 1.445 angstroms; (across all 143 pairs:
18.673)
> show #2 models
> save "/Users/prash_mbp/Dropbox (VU Basic Sciences)/[FiguresOnly__C-
> ring]/Figures/FSM/CW.cxs" includeMaps true
> close session
> open "/Users/prash_mbp/Downloads/cryosparc_P11_J406_009_volume_map (1).mrc"
Opened cryosparc_P11_J406_009_volume_map (1).mrc as #1, grid size 768,768,768,
pixel 1.36, shown at step 1, values float32
> open "/Users/prash_mbp/Downloads/cryosparc_P11_J405_008_volume_map (1).mrc"
Opened cryosparc_P11_J405_008_volume_map (1).mrc as #2, grid size 768,768,768,
pixel 1.36, shown at step 1, values float32
> view orient
> volume #1 level -0.01938,0 level 0.2138,0.8 level 0.2875,1
> tile
2 models tiled
> volume #2 color #f8fff9 color #ffffb3 color #ffffb3
> volume #2 color silver color #ffffb3 color #ffffb3
> volume #2 color white color #ffffb3 color #ffffb3
> volume #2 color #5e5e5e color #ffffb3 color #ffffb3
> volume #2 color black color #ffffb3 color #ffffb3
> volume #2 color #00fdff color #ffffb3 color #ffffb3
> volume #2 color white color #ffffb3 color #ffffb3
> volume #2 color #919191 color #ffffb3 color #ffffb3
> volume #2 color #929292 color #ffffb3 color #ffffb3
> volume #2 color white color #ffffb3 color #ffffb3
> volume #2 color #929000 color #ffffb3 color #ffffb3
> volume #2 color #008f00 color #ffffb3 color #ffffb3
> volume #2 color #fffb00 color #ffffb3 color #ffffb3
> volume #2 color white color #ffffb3 color #ffffb3
> volume #2 color #ebebeb color #ffffb3 color #ffffb3
> volume #2 color white color #ffffb3 color #ffffb3
> volume #2 color black color #ffffb3 color #ffffb3
> volume #2 color white color #ffffb3 color #ffffb3
> view
> view orient
> volume #1 region 0,0,0,767,767,767 step 4
> volume #1 region 0,0,0,767,767,767 step 1 colorMode opaque8 showOutlineBox
> true imageMode "box faces"
> volume #1 orthoplanes xyz positionPlanes 383,383,383 imageMode orthoplanes
> volume #2 region 0,0,0,767,767,767 step 4
> volume #2 region 0,0,0,767,767,767 step 1 colorMode opaque8 showOutlineBox
> true orthoplanes xyz positionPlanes 383,383,383 imageMode orthoplanes
> view orient
> volume #2 step 2
> volume #2 step 1
> volume #2 orthoplanes xyz positionPlanes 468,383,383
> volume #2 orthoplanes xyz positionPlanes 585,383,383
> view orient
> view
> view orient
> volume #2 orthoplanes xyz positionPlanes 585,533,383
> volume #1 orthoplanes xyz positionPlanes 383,259,383
> volume #1 orthoplanes xyz positionPlanes 383,244,383
> volume #1 orthoplanes xyz positionPlanes 383,364,383
> volume #1 orthoplanes xyz positionPlanes 383,462,383
> volume #1 orthoplanes xyz positionPlanes 383,529,383
> volume #1 orthoplanes xyz positionPlanes 383,534,383
> volume #1 orthoplanes xyz positionPlanes 383,539,383
> volume #2 orthoplanes xyz positionPlanes 585,535,383
> volume #2 orthoplanes xyz positionPlanes 585,539,383
> volume #2 orthoplanes xyz positionPlanes 292,539,383
> volume #2 orthoplanes xyz positionPlanes 318,539,383
> volume #2 orthoplanes xyz positionPlanes 283,539,383
> volume #2 orthoplanes xyz positionPlanes 283,640,383
> volume #2 orthoplanes xyz positionPlanes 283,615,383
> volume #2 orthoplanes xyz positionPlanes 283,626,383
> volume #2 orthoplanes xyz positionPlanes 277,626,383
> volume #2 orthoplanes xyz positionPlanes 294,626,383
> volume #2 orthoplanes xyz positionPlanes 675,626,383
> volume #1
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.7.dev202305160152 (2023-05-16)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple
Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro18,1
Model Number: MK183LL/A
Chip: Apple M1 Pro
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 16 GB
System Firmware Version: 8422.141.2
OS Loader Version: 8422.141.2
Software:
System Software Overview:
System Version: macOS 13.5 (22G74)
Kernel Version: Darwin 22.6.0
Time since boot: 23 days, 17 hours, 2 minutes
Graphics/Displays:
Apple M1 Pro:
Chipset Model: Apple M1 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
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
DELL U3421WE:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 60.00Hz
Mirror: Off
Online: Yes
Rotation: Supported
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: 1.5.11
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: 1.45.6
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: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.3
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.dev202305160152
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: 1.1.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-ListInfo: 1.2
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: 2.1
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: 1.10.2
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-QScore: 1.0
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: 1.11.1
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: 1.2.2
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2.1
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: 4.39.4
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: 3.5.1
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.2
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
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