![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 2 years ago
Closed 2 years ago
#9663 closed defect (limitation)
Graphics crash, macOS 13.5, Apple M1 Pro
| 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 (last modified by )
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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===== 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
Duplicate atom serial number found: 2
Duplicate atom serial number found: 3
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Ignored bad PDB record found on line 6777
Duplicate atom serial number found: 235
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Ignored bad PDB record found on line 9773
Duplicate atom serial number found: 3229
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[deleted to fit within ticket limits]
Duplicate atom serial number found: 3229
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Duplicate atom serial number found: 5771
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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
Ignored bad PDB record found on line 195439
Duplicate atom serial number found: 5771
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384 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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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
Change History (4)
comment:1 by , 2 years ago
| Component: | Unassigned → Volume Data |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash during volume command |
comment:2 by , 2 years ago
comment:3 by , 2 years ago
| Component: | Volume Data → Graphics |
|---|---|
| Summary: | Crash during volume command → Graphics crash, macOS 13.5, Apple M1 Pro |
From reporter:
Dear all, This crash happened because I opened two large cryoEM maps (1.4gb each) in ortho view, tiled on my Mac Pro M1 laptop so this probably was due to limitations of RAM (16gb). You can disregard this crash. Thank you Prash
comment:4 by , 2 years ago
| Resolution: | → limitation |
|---|---|
| Status: | assigned → closed |
The crash report shows it crashed in Apple's OpenGL graphics driver. I've never seen this happen on an Apple M1 or M2 machine although Apple's graphics drivers often crash on Intel Macs.
You are right that the crash was due to too much memory use. The crash report shows ChimeraX using 60 Gbytes of memory on your machine with 16 Gbytes of physical memory.
Thanks for reporting the crash. We like to keep tabs on how stable ChimeraX when lots of memory is being used. Once you get close to the memory limit of what the operating system will give you the program can crash anywhere.
Note:
See TracTickets
for help on using tickets.
Dear all, This crash happened because I opened two large cryoEM maps (1.4gb each) in ortho view, tiled on my Mac Pro M1 laptop so this probably was due to limitations of RAM (16gb). You can disregard this crash. Thank you Prash ________________________________ From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> Sent: Wednesday, August 30, 2023 11:50:35 AM To: Singh, Prashant Kumar <Prashant.k.singh@vanderbilt.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu> Subject: Re: [ChimeraX] #9663: Crash during volume command (was: ChimeraX bug report submission) #9663: Crash during volume command -----------------------------------------+------------------------- Reporter: Prashant.k.singh@… | Owner: Tom Goddard Type: defect | Status: assigned Priority: normal | Milestone: Component: Volume Data | Version: Resolution: | Keywords: Blocked By: | Blocking: Notify when closed: | Platform: all Project: ChimeraX | -----------------------------------------+------------------------- Changes (by pett): * component: Unassigned => Volume Data * owner: (none) => Tom Goddard * platform: => all * project: => ChimeraX * status: new => assigned * summary: ChimeraX bug report submission => Crash during volume command Old description: > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > New 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 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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 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 [deleted to fit within ticket limits] 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 175361 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 175819 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 176210 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 176581 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 176817 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 179813 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 181901 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 182359 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 182750 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 183121 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 183357 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 186353 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 188441 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 188899 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 189290 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 189661 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 189897 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 192893 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 194981 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 195439 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 195830 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 196201 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 196437 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 199433 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 201521 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 201979 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 202370 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 202741 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 202977 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 205973 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 208061 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 208519 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 208910 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 209281 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 209517 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 212513 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 214601 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 215059 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 215450 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 215821 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 216057 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 219053 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 221141 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 221599 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 221990 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 222361 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 > 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 }}} -- -- Ticket URL: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F9663%23comment%3A1&data=05%7C01%7CPrashant.k.singh%40vanderbilt.edu%7C697c90a1b7e94c841b7908dba9794bbe%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638290110814250660%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vMcOyvsudkI%2BobLiMVMh3sKz2dbTX7f5MkwsHuZXRrY%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/9663#comment:1>> ChimeraX <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Fchimerax%2F&data=05%7C01%7CPrashant.k.singh%40vanderbilt.edu%7C697c90a1b7e94c841b7908dba9794bbe%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638290110814250660%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Pn8Q0NZHStfP52GnU11iVT1MyDF6%2FJCZwgLfe5Eazek%3D&reserved=0<https://www.rbvi.ucsf.edu/chimerax/>> ChimeraX Issue Tracker