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Opened 2 years ago
Closed 2 years ago
#9868 closed defect (can't reproduce)
Failed to lock QIOSurfaceGraphicsBuffer
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4.dev202203190100 (2022-03-19 01:00:21 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Illegal instruction
Thread 0x00000003228ed000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003218ea000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003208e7000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py", line 416 in select
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031f8e4000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031e8e1000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031d8de000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031c8db000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031b8d8000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x000000031a8d5000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003198d2000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00000003188cf000 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 910 in run
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x000000020473b2c0 (most recent call first):
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py", line 318 in event_loop
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py", line 87 in _run_code
File "/private/var/folders/3p/228qm2qs1k36b0cm90mx3_sw0000gn/T/AppTranslocation/291E0C34-CB87-4B6C-B05E-E55FCF338A00/d/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":"2023-09-27 14:36:50.00 -0700","app_version":"1.4.0","slice_uuid":"9596eff5-d2be-396c-9c4e-6177235c3dae","build_version":"1.4.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":1,"is_first_party":0,"bug_type":"309","os_version":"macOS 13.2.1 (22D68)","roots_installed":0,"name":"ChimeraX","incident_id":"A73703E4-FF31-45FD-91B6-49A5751966EE"}
{
"uptime" : 34000,
"procRole" : "Background",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "MacBookPro17,1",
"coalitionID" : 3191,
"osVersion" : {
"train" : "macOS 13.2.1",
"build" : "22D68",
"releaseType" : "User"
},
"captureTime" : "2023-09-27 14:36:44.8108 -0700",
"incident" : "A73703E4-FF31-45FD-91B6-49A5751966EE",
"pid" : 3791,
"translated" : true,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2023-09-26 17:45:11.0108 -0700",
"procStartAbsTime" : 282702051697,
"procExitAbsTime" : 825450088057,
"procName" : "ChimeraX",
"procPath" : "\/Volumes\/VOLUME\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.4.0","CFBundleVersion":"1.4.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"2A554CB2-D81E-5AB0-8057-FC287B0A43CC","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "1588EBE2-4379-A243-BF8B-E4CFCCEE94E9",
"throttleTimeout" : 2147483647,
"wakeTime" : 3,
"sleepWakeUUID" : "4A504FB8-F280-4CFA-897E-8921A226257E",
"sip" : "enabled",
"exception" : {"codes":"0x0000000000000001, 0x0000000000000000","rawCodes":[1,0],"type":"EXC_BAD_INSTRUCTION","signal":"SIGILL"},
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
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===== Log before crash start =====
UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/holoenzyme hCaW196R_RIa R333K/flipback_hetdimer.mrc"
Opened flipback_hetdimer.mrc as #1, grid size 38,41,46, pixel 3.33,3.33,3.33,
shown at level 0.36, step 1, values float32
> volume #1 level 0.2196
> volume #1 level 0.334
> volume #1 level 0.3577
> volume #1 level 0.3883
> volume #1 level 0.3566
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/holoenzyme hCaW196R_RIa R333K/flipback_hetdimer
> (1).pdb"
Chain information for flipback_hetdimer (1).pdb #2
---
Chain | Description
A | No description available
X | No description available
> hide #!1 models
> set bgColor white
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 2/A
> select /A:13-14
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /A:13-204
1587 atoms, 1623 bonds, 192 residues, 1 model selected
> select /A:303
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:302-303
22 atoms, 23 bonds, 2 residues, 1 model selected
> ui tool show "Blast Protein"
> blastprotein /A database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name
> bp1
Webservices job id: KDLD59KE9GFXB08R
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 14 atom styles
> style sel ball
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> show sel atoms
> show sel surfaces
> show sel cartoons
> show sel atoms
> hide sel surfaces
> ui mousemode right zoom
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/cryosparc_P2_J139_001_volume_map.mrc"
Opened cryosparc_P2_J139_001_volume_map.mrc as #3, grid size 128,128,128,
pixel 1.9, shown at level 0.0121, step 1, values float32
> select add #3
14 atoms, 15 bonds, 1 residue, 4 models selected
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 5 models selected
> select subtract #2
3 models selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,-52.688,0,1,0,-80.094,0,0,1,-145.26
> view matrix models #3,1,0,0,-56.654,0,1,0,-100.93,0,0,1,-174.49
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 4 models selected
> select subtract #3
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 3 models selected
> view matrix models #2,1,0,0,24.085,0,1,0,-10.985,0,0,1,64.645
> select subtract #2
1 model selected
> select add #3
2 models selected
> volume #3 level 0.02462
> view matrix models #3,1,0,0,-44.352,0,1,0,-130.58,0,0,1,-161.21
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.79002,-0.056233,-0.6105,63.359,-0.48137,0.55978,-0.67448,66.238,0.37967,0.82673,0.41517,-239.28
> view matrix models
> #3,0.75092,-0.18044,-0.63526,86.581,-0.47648,0.51802,-0.71037,75.15,0.45725,0.83612,0.30301,-236.47
> view matrix models
> #3,0.1022,-0.78041,-0.61686,239.52,-0.67992,0.39784,-0.61597,103.92,0.72612,0.48237,-0.48996,-129.82
> view matrix models
> #3,-0.98071,-0.19545,-0.0009505,227.94,-0.17272,0.86892,-0.46383,-36.21,0.091484,-0.45472,-0.88592,113.44
> view matrix models
> #3,-0.81508,-0.57388,0.079479,244.01,-0.56085,0.7472,-0.35656,14.316,0.14524,-0.3352,-0.93088,97.466
> view matrix models
> #3,-0.72894,-0.51442,-0.45169,290.7,-0.037919,0.68913,-0.72364,0.75346,0.68353,-0.51037,-0.52184,1.7199
> view matrix models
> #3,-0.074648,-0.95635,-0.28253,242.56,-0.27276,0.2921,-0.91667,102.64,0.95918,0.0086345,-0.28266,-125.93
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.074648,-0.95635,-0.28253,247.26,-0.27276,0.2921,-0.91667,116.15,0.95918,0.0086345,-0.28266,-100.44
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #3,-0.074648,-0.95635,-0.28253,259.84,-0.27276,0.2921,-0.91667,94.672,0.95918,0.0086345,-0.28266,-27.137
> ui tool show "Fit in Map"
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.05093, steps = 108
shifted from previous position = 9.4
rotated from previous position = 21.1 degrees
atoms outside contour = 3015, contour level = 0.024615
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.29378473 -0.49848044 0.81560271 137.08527599
-0.94940490 0.25125346 -0.18841983 193.99411200
-0.11099940 -0.82969208 -0.54707420 121.99586260
Axis -0.52834586 0.76342987 -0.37151782
Axis point 165.18429441 0.00000000 74.29225667
Rotation angle (degrees) 142.63662752
Shift along axis 30.34882418
> color #3 #ffffb261 models
> color #3 #ffffb254 models
> select subtract #3
Nothing selected
> ui mousemode right zoom
> volume #3 level 0.02462
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.05093, steps = 36
shifted from previous position = 0.00527
rotated from previous position = 0.0174 degrees
atoms outside contour = 3015, contour level = 0.024615
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.29376450 -0.49834870 0.81569050 137.08295966
-0.94943441 0.25103723 -0.18855932 193.98994804
-0.11080039 -0.82983666 -0.54689523 121.98399704
Axis -0.52835976 0.76335226 -0.37165750
Axis point 165.18831934 0.00000000 74.30930524
Rotation angle (degrees) 142.63743111
Shift along axis 30.31727756
> volume #3 level 0.05266
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.73456,-0.39363,0.5527,37.875,0.15633,0.8908,0.42665,-16.771,-0.66029,-0.227,0.71588,99.696
> view matrix models
> #2,-0.32214,-0.83816,0.44012,103.42,0.074832,0.44091,0.89443,-19.195,-0.94373,0.32107,-0.079313,129.28
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.32214,-0.83816,0.44012,102.21,0.074832,0.44091,0.89443,-12.272,-0.94373,0.32107,-0.079313,125.24
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.06159, steps = 160
shifted from previous position = 6.63
rotated from previous position = 48.3 degrees
atoms outside contour = 3219, contour level = 0.052655
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.94142895 -0.33520250 -0.03675354 178.48497876
-0.20705056 0.66062920 -0.72159485 147.29478215
0.26616086 -0.67172044 -0.69133932 91.35292844
Axis 0.14992281 -0.91056269 0.38522557
Axis point 95.88871198 0.00000000 85.53974950
Rotation angle (degrees) 170.42528326
Shift along axis -72.17067934
> view matrix models
> #2,0.19309,-0.41699,0.88816,78.969,-0.047675,0.90014,0.43298,5.1131,-0.98002,-0.12595,0.15393,119.78
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.66784,-0.70326,0.24375,134.55,-0.28676,0.54531,0.78766,15.211,-0.68684,0.45614,-0.56585,110.24
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.66784,-0.70326,0.24375,136.73,-0.28676,0.54531,0.78766,16.889,-0.68684,0.45614,-0.56585,107.87
> ui mousemode right zoom
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.77688,-0.62962,-0.0053813,145.82,-0.40146,0.48874,0.77457,23.872,-0.48506,0.60391,-0.63246,96.513
> ui mousemode right "translate selected models"
> view matrix models
> #2,-0.77688,-0.62962,-0.0053813,143.62,-0.40146,0.48874,0.77457,23.554,-0.48506,0.60391,-0.63246,97.654
> view matrix models
> #2,-0.77688,-0.62962,-0.0053813,145.64,-0.40146,0.48874,0.77457,26.346,-0.48506,0.60391,-0.63246,92.396
> view matrix models
> #2,-0.77688,-0.62962,-0.0053813,143.19,-0.40146,0.48874,0.77457,25.169,-0.48506,0.60391,-0.63246,94.185
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.041321,-0.72568,0.68679,90.008,-0.14613,0.68437,0.71434,10.896,-0.9884,-0.070841,-0.13432,117.04
> view matrix models
> #2,0.76604,-0.13176,0.62914,44.25,-0.17214,0.90096,0.39829,16.696,-0.61931,-0.41341,0.66749,84.849
> view matrix models
> #2,0.96243,-0.19645,0.18746,30.523,0.041942,0.78962,0.61216,-0.13741,-0.26828,-0.5813,0.76819,57.92
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.96243,-0.19645,0.18746,30.297,0.041942,0.78962,0.61216,-1.0603,-0.26828,-0.5813,0.76819,63.591
> view matrix models
> #2,0.96243,-0.19645,0.18746,26.634,0.041942,0.78962,0.61216,-3.2555,-0.26828,-0.5813,0.76819,63.741
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.06016, steps = 124
shifted from previous position = 5.09
rotated from previous position = 24.7 degrees
atoms outside contour = 3237, contour level = 0.052655
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.35609382 -0.68376823 0.63691303 132.76435885
-0.92725360 0.17413081 -0.33148035 186.53007699
0.11574955 -0.70861800 -0.69603346 104.09621171
Axis -0.54828955 0.75767691 -0.35398344
Axis point 147.37033065 0.00000000 78.04754571
Rotation angle (degrees) 159.88399714
Shift along axis 31.68788612
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.88066,0.084716,0.46612,39.851,-0.27982,0.88694,0.36748,19.614,-0.38228,-0.45406,0.80479,74.531
> volume #3 level 0.05266
> volume #3 level 0.03463
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.06015, steps = 56
shifted from previous position = 3.77
rotated from previous position = 0.0373 degrees
atoms outside contour = 2961, contour level = 0.034629
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.35617066 -0.68382777 0.63680612 132.76394754
-0.92714560 0.17374686 -0.33198352 186.50488296
0.11637649 -0.70865479 -0.69589144 104.05750959
Axis -0.54830583 0.75756934 -0.35418838
Axis point 147.35052728 0.00000000 78.07803663
Rotation angle (degrees) 159.91056850
Shift along axis 31.63917348
> hide #!3 models
> select /X
2117 atoms, 2155 bonds, 267 residues, 1 model selected
> color sel cornflower blue
> color sel purple
> color sel hot pink
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/cryosparc_P2_J77_003_volume_map.mrc"
Opened cryosparc_P2_J77_003_volume_map.mrc as #4, grid size 128,128,128, pixel
1.9, shown at level 0.0217, step 1, values float32
> ui mousemode right zoom
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected
> select subtract #2
1 model selected
> select add #4
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #4,1,0,0,-20.836,0,1,0,-68.443,0,0,1,-117
> view matrix models #4,1,0,0,-25.221,0,1,0,-82.034,0,0,1,-140.68
> ui mousemode right "rotate selected models"
> view matrix models
> #4,-0.044338,-0.5894,-0.80662,267.96,-0.45672,0.73006,-0.50835,66.432,0.88851,0.34586,-0.30156,-131.42
> view matrix models
> #4,-0.18322,-0.83702,0.51558,155.33,-0.68629,0.48441,0.54254,-2.9827,-0.70387,-0.25443,-0.6632,174.42
> view matrix models
> #4,-0.53398,-0.77518,-0.3376,292.2,0.45572,-0.60019,0.65734,-19.459,-0.71217,0.19715,0.67375,-41.047
> volume #4 level 0.0849
> view matrix models
> #4,-0.78371,-0.57972,-0.22298,284.57,0.28505,-0.65465,0.70013,3.0711,-0.55185,0.48514,0.6783,-97.154
> volume #4 level 0.186
> ui mousemode right "translate selected models"
> view matrix models
> #4,-0.78371,-0.57972,-0.22298,279.51,0.28505,-0.65465,0.70013,-9.4399,-0.55185,0.48514,0.6783,-120.78
> view matrix models
> #4,-0.78371,-0.57972,-0.22298,340.7,0.28505,-0.65465,0.70013,-42.227,-0.55185,0.48514,0.6783,-50.205
> view matrix models
> #4,-0.78371,-0.57972,-0.22298,290.59,0.28505,-0.65465,0.70013,-72.535,-0.55185,0.48514,0.6783,-14.639
> ui mousemode right "rotate selected models"
> fitmap #2 inMap #4
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J77_003_volume_map.mrc (#4) using 5098 atoms
average map value = 0.1274, steps = 312
shifted from previous position = 13.4
rotated from previous position = 58.3 degrees
atoms outside contour = 3496, contour level = 0.18604
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J77_003_volume_map.mrc (#4) coordinates:
Matrix rotation and translation
0.39366624 0.59082543 -0.70423874 98.72670212
-0.68342782 -0.32424308 -0.65405875 151.96230908
-0.61477908 0.73877719 0.27614298 185.24165720
Axis 0.73698981 -0.04733570 -0.67424428
Axis point -0.00000000 8.99711411 209.82744806
Rotation angle (degrees) 109.09994115
Shift along axis -59.33079535
> ui mousemode right zoom
> select subtract #4
Nothing selected
> volume #4 color #b2ffff51
> volume #4 color #b2ffff52
> volume #4 level 0.2073
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/cryosparc_P2_J87_002_volume_map.mrc"
Opened cryosparc_P2_J87_002_volume_map.mrc as #5, grid size 128,128,128, pixel
1.9, shown at level 0.0297, step 1, values float32
> hide #!2 models
> hide #!4 models
> volume #5 level 0.05848
> volume #5 level 0.1277
> volume #5 level 0.1997
> volume #5 level 0.2459
> show #!2 models
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.22476,-0.4398,0.86952,108.59,0.12919,0.89792,0.42077,2.9535,-0.96581,0.017763,0.25864,145.08
> ui mousemode right "rotate selected models"
> view matrix models
> #2,-0.74892,-0.61014,0.25856,173.69,0.59433,-0.4459,0.66928,-50.862,-0.29307,0.65491,0.69657,108.37
> view matrix models
> #2,-0.9943,-0.033639,0.10122,200.01,0.068816,-0.92735,0.36781,-22.002,0.081491,0.37268,0.92438,77.781
> view matrix models
> #2,-0.066109,-0.62352,0.77901,125.75,0.91541,-0.34856,-0.20131,-69.798,0.39705,0.6998,0.59382,61.953
> view matrix models
> #2,0.92421,-0.21728,0.31404,65.162,0.37945,0.42982,-0.81932,-19.522,0.043043,0.87638,0.47969,89.249
> view matrix models
> #2,0.32734,0.78112,-0.53169,123.53,-0.64369,-0.22759,-0.73066,39.961,-0.69174,0.58142,0.4283,135
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.32734,0.78112,-0.53169,144.97,-0.64369,-0.22759,-0.73066,57.339,-0.69174,0.58142,0.4283,143.42
> view matrix models
> #2,0.32734,0.78112,-0.53169,131.98,-0.64369,-0.22759,-0.73066,46.342,-0.69174,0.58142,0.4283,139.13
> view matrix models
> #2,0.32734,0.78112,-0.53169,87.732,-0.64369,-0.22759,-0.73066,140.3,-0.69174,0.58142,0.4283,190.72
> view matrix models
> #2,0.32734,0.78112,-0.53169,107.92,-0.64369,-0.22759,-0.73066,137.64,-0.69174,0.58142,0.4283,188.27
> fitmap #2 inMap #5
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J87_002_volume_map.mrc (#5) using 5098 atoms
average map value = 0.1252, steps = 140
shifted from previous position = 11.6
rotated from previous position = 15.9 degrees
atoms outside contour = 4024, contour level = 0.24585
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J87_002_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.36600272 0.59827985 -0.71281360 100.71411204
-0.63516086 -0.39922110 -0.66120587 146.17749312
-0.68015637 0.69475445 0.23388794 188.29332461
Axis 0.73961915 -0.01781314 -0.67278987
Axis point 0.00000000 7.25894503 204.23978094
Rotation angle (degrees) 113.55725141
Shift along axis -54.79563603
> ui mousemode right zoom
> volume #5 color #b2b2ff51
> volume #5 color #b2b2ff52
> volume #5 color #19192152
> volume #5 color #393a4b52
> volume #5 color #393a4b3f
> select subtract #2
1 model selected
> fitmap #2 inMap #5
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J87_002_volume_map.mrc (#5) using 5098 atoms
average map value = 0.1252, steps = 44
shifted from previous position = 0.0428
rotated from previous position = 0.00667 degrees
atoms outside contour = 4023, contour level = 0.24585
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J87_002_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.36600862 0.59836584 -0.71273840 100.69519040
-0.63514354 -0.39915343 -0.66126336 146.15604994
-0.68016938 0.69471927 0.23395460 188.32529532
Axis 0.73960666 -0.01776443 -0.67280489
Axis point -0.00000000 7.23374201 204.24684075
Rotation angle (degrees) 113.55286922
Shift along axis -54.82772575
> volume #5 level 0.2055
> volume #5 level 0.243
> fitmap #2 inMap #5
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J87_002_volume_map.mrc (#5) using 5098 atoms
average map value = 0.1252, steps = 48
shifted from previous position = 0.00828
rotated from previous position = 0.0321 degrees
atoms outside contour = 4002, contour level = 0.24297
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J87_002_volume_map.mrc (#5) coordinates:
Matrix rotation and translation
0.36623911 0.59849787 -0.71250910 100.68754770
-0.63471780 -0.39924714 -0.66161548 146.12130127
-0.68044267 0.69455167 0.23365734 188.33473421
Axis 0.73973553 -0.01749097 -0.67267036
Axis point 0.00000000 7.18817744 204.20538771
Rotation angle (degrees) 113.55788430
Shift along axis -54.76084090
> select /A
2981 atoms, 2893 bonds, 11 pseudobonds, 499 residues, 2 models selected
> select /X
2117 atoms, 2155 bonds, 267 residues, 1 model selected
> color sel purple
> select /A:13
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /A:13-83
572 atoms, 581 bonds, 71 residues, 1 model selected
> select /A:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:13-83
572 atoms, 581 bonds, 71 residues, 1 model selected
> select /A:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:83
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> color (#!2 & sel) red
> style sel sphere
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> style sel ball
Changed 14 atom styles
> style sel sphere
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> show sel surfaces
> hide sel surfaces
> color (#!2 & sel) forest green
> surface (#!2 & sel)
> hide sel surfaces
> select /X
2117 atoms, 2155 bonds, 267 residues, 1 model selected
> color sel hot pink
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/data
> analysis/cryosparc_P2_J93_class_00_00042_volume_sharp.mrc"
Opened cryosparc_P2_J93_class_00_00042_volume_sharp.mrc as #6, grid size
128,128,128, pixel 1.9, shown at level 0.0874, step 1, values float32
> hide #!6 models
> open "/Users/hoangnguyen/Library/CloudStorage/OneDrive-UCSanDiego/Susan
> Taylor lab/PKA project/cryosparc_P2_J113_001_volume_map.mrc"
Opened cryosparc_P2_J113_001_volume_map.mrc as #7, grid size 128,128,128,
pixel 1.9, shown at level 0.0245, step 1, values float32
> hide #!5 models
> volume #7 level 0.123
> volume #7 level 0.1723
> volume #7 level 0.2172
> fitmap #2 inMap #7
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J113_001_volume_map.mrc (#7) using 5098 atoms
average map value = 0.1267, steps = 148
shifted from previous position = 2.04
rotated from previous position = 6.86 degrees
atoms outside contour = 3811, contour level = 0.21723
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J113_001_volume_map.mrc (#7) coordinates:
Matrix rotation and translation
0.39057817 0.58373066 -0.71183370 98.62046944
-0.70449973 -0.30820089 -0.63929050 154.18215555
-0.59256124 0.75117956 0.29086155 184.35062168
Axis 0.73211332 -0.06279959 -0.67828187
Axis point 0.00000000 11.22910299 212.05667907
Rotation angle (degrees) 108.26307881
Shift along axis -62.52290126
> volume #7 color #ffb2b221
> volume #7 color #100d0d21
> volume #7 color #00000021
> volume #7 color #0000001e
> volume #7 color #00000022
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected
> select subtract #2
1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:196-197
25 atoms, 26 bonds, 2 residues, 1 model selected
> select /A:197
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /A:196-197
25 atoms, 26 bonds, 2 residues, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 14 atom styles
> select /A:196-197
25 atoms, 26 bonds, 2 residues, 1 model selected
> select /A:196-197
25 atoms, 26 bonds, 2 residues, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:196-197
25 atoms, 26 bonds, 2 residues, 1 model selected
> select clear
> hide atoms
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> select /A:196
14 atoms, 15 bonds, 1 residue, 1 model selected
> style sel sphere
Changed 14 atom styles
> style sel sphere
Changed 14 atom styles
> show sel surfaces
> hide sel surfaces
> show sel cartoons
> hide sel cartoons
> style sel ball
Changed 14 atom styles
> show sel cartoons
> show sel atoms
> style sel sphere
Changed 14 atom styles
> style sel sphere
Changed 14 atom styles
> style sel stick
Changed 14 atom styles
> color (#!2 & sel) red
> color (#!2 & sel) blue
> color (#!2 & sel) purple
> color (#!2 & sel) red
> ui tool show "Show Sequence Viewer"
> sequence chain /X
Alignment identifier is 2/X
> select /X:333
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /X:333
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel red
> hide #!2 models
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected
> select subtract #2
1 model selected
> select add #7
2 models selected
> select subtract #7
Nothing selected
> show #!2 models
> show #!3 models
> select add #3
2 models selected
> select subtract #3
Nothing selected
> hide #!7 models
> ui mousemode right "translate selected models"
> select add #3
2 models selected
> view matrix models
> #3,-0.074648,-0.95635,-0.28253,276.53,-0.27276,0.2921,-0.91667,100.86,0.95918,0.0086345,-0.28266,-19.251
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.3773,-0.55695,-0.7399,223.28,-0.89686,-0.41889,-0.14202,177.74,-0.23084,0.71717,-0.65755,84.057
> view matrix models
> #3,0.62876,-0.16127,-0.76069,143.86,-0.388,-0.91284,-0.12719,175.13,-0.67388,0.37512,-0.63653,180.62
> view matrix models
> #3,0.8915,-0.21096,-0.4009,74.618,-0.26493,-0.96063,-0.083633,160.63,-0.36748,0.18077,-0.91229,199.68
> view matrix models
> #3,0.88975,-0.16358,-0.42613,71.795,-0.23866,-0.96252,-0.12883,162.94,-0.38908,0.21633,-0.89544,195.86
> ui mousemode right "translate selected models"
> view matrix models
> #3,0.88975,-0.16358,-0.42613,132.26,-0.23866,-0.96252,-0.12883,203.09,-0.38908,0.21633,-0.89544,207.64
> view matrix models
> #3,0.88975,-0.16358,-0.42613,101.95,-0.23866,-0.96252,-0.12883,280.72,-0.38908,0.21633,-0.89544,266.33
> view matrix models
> #3,0.88975,-0.16358,-0.42613,96.156,-0.23866,-0.96252,-0.12883,280.56,-0.38908,0.21633,-0.89544,263.96
> ui mousemode right "rotate selected models"
> view matrix models
> #3,0.43696,-0.85083,-0.29182,224.47,-0.89926,-0.42045,-0.12066,293.32,-0.020031,0.31515,-0.94883,211.48
> view matrix models
> #3,-0.39973,-0.88665,-0.23254,326.82,-0.87374,0.44525,-0.19579,188.8,0.27713,0.12492,-0.95268,198.93
> view matrix models
> #3,-0.94979,-0.043862,-0.3098,297.57,0.021627,0.97855,-0.20485,9.7963,0.31214,-0.20127,-0.92847,233.21
> view matrix models
> #3,-0.21573,0.29563,-0.93063,235.99,0.82921,0.55875,-0.014727,-60.46,0.51563,-0.77486,-0.36568,214.03
> view matrix models
> #3,0.038708,-0.73188,-0.68033,305.28,-0.61711,0.51798,-0.59234,194.4,0.78592,0.44277,-0.4316,32.936
> view matrix models
> #3,0.9344,0.34936,0.069565,-33.524,0.34675,-0.8473,-0.40231,224.97,-0.08161,0.40004,-0.91286,204.12
> view matrix models
> #3,0.19066,0.97371,0.12462,-26.379,0.98165,-0.18935,-0.022342,16.605,0.0018417,0.12659,-0.99195,237.86
> view matrix models
> #3,-0.48477,0.84051,-0.24197,118.66,0.80173,0.53759,0.26119,-87.037,0.34961,-0.06738,-0.93447,212.18
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.0614, steps = 100
shifted from previous position = 21.3
rotated from previous position = 21.9 degrees
atoms outside contour = 2872, contour level = 0.034629
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.94646621 -0.31941109 0.04667200 179.16600157
-0.22422298 0.54650840 -0.80687832 151.03200437
0.23221925 -0.77414800 -0.58887104 95.16030130
Axis 0.15505241 -0.87898758 0.45093190
Axis point 99.19680830 0.00000000 92.00400008
Rotation angle (degrees) 173.94137523
Shift along axis -62.06432087
> select subtract #3
Nothing selected
> ui mousemode right zoom
> volume #3 color #49493954
> select add #2
5098 atoms, 5048 bonds, 11 pseudobonds, 766 residues, 2 models selected
> ui mousemode right "translate selected models"
> view matrix models
> #2,0.21416,0.8015,-0.55832,133.01,-0.8187,-0.16448,-0.55016,161.41,-0.53279,0.57492,0.62097,177.63
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.0614, steps = 72
shifted from previous position = 3.55
rotated from previous position = 0.00786 degrees
atoms outside contour = 2873, contour level = 0.034629
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.94648466 -0.31935511 0.04668087 179.17256337
-0.22422557 0.54661287 -0.80680684 151.03507502
0.23214152 -0.77409734 -0.58896827 95.16521404
Axis 0.15503143 -0.87901774 0.45088032
Axis point 99.19987136 0.00000000 91.99864336
Rotation angle (degrees) 173.94442183
Shift along axis -62.07701012
> volume #3 level 0.01861
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.0614, steps = 44
shifted from previous position = 0.0317
rotated from previous position = 0.0109 degrees
atoms outside contour = 2549, contour level = 0.018607
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.94653338 -0.31920084 0.04674819 179.15137286
-0.22420415 0.54668375 -0.80676476 151.04794544
0.23196352 -0.77411091 -0.58902056 95.18695634
Axis 0.15497641 -0.87903893 0.45085792
Axis point 99.18958904 0.00000000 92.00148022
Rotation angle (degrees) 173.95260840
Shift along axis -62.09699446
> volume #3 level 0.02462
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.0614, steps = 76
shifted from previous position = 0.0304
rotated from previous position = 0.0134 degrees
atoms outside contour = 2680, contour level = 0.024615
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.94647583 -0.31938887 0.04662890 179.17030664
-0.22421381 0.54664835 -0.80678606 151.03562989
0.23218888 -0.77405835 -0.58900084 95.16305799
Axis 0.15503644 -0.87902748 0.45085961
Axis point 99.19720649 0.00000000 91.99839384
Rotation angle (degrees) 173.94123400
Shift along axis -62.08136327
> volume #3 level 0.03864
> fitmap #2 inMap #3
Fit molecule flipback_hetdimer (1).pdb (#2) to map
cryosparc_P2_J139_001_volume_map.mrc (#3) using 5098 atoms
average map value = 0.0614, steps = 40
shifted from previous position = 0.0206
rotated from previous position = 0.0153 degrees
atoms outside contour = 2942, contour level = 0.038635
Position of flipback_hetdimer (1).pdb (#2) relative to
cryosparc_P2_J139_001_volume_map.mrc (#3) coordinates:
Matrix rotation and translation
-0.94652531 -0.31922142 0.04677096 179.15789005
-0.22419175 0.54653311 -0.80687026 151.03792152
0.23200839 -0.77420879 -0.58887423 95.17923569
Axis 0.15498649 -0.87899585 0.45093845
Axis point 99.19305835 0.00000000 92.00521562
Rotation angle (degrees) 173.95158637
Shift along axis -62.07467665
> select subtract #2
1 model selected
> select /X:113
11 atoms, 10 bonds, 1 residue, 1 model selected
> select /X:113-333
1757 atoms, 1789 bonds, 221 residues, 1 model selected
> color sel cyan
> color sel cornflower blue
> color sel blue
> color sel cyan
> select clear
Failed to lock QIOSurfaceGraphicsBuffer(0x600000270420, surface=0x0,
size=QSize(-2147483648, -2147483648), isLocked=false, isInUse=false)
-536870206
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.4.dev202203190100 (2022-03-19)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple
Locale: UTF-8
Qt version: PyQt6 6.2.3, Qt 6.2.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro17,1
Model Number: MJ123LL/A
Chip: Unknown
Total Number of Cores: 8 (4 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 8419.80.7
OS Loader Version: 8419.80.7
Software:
System Software Overview:
System Version: macOS 13.2.1 (22D68)
Kernel Version: Darwin 22.3.0
Time since boot: 1 day, 5 hours, 35 minutes
Graphics/Displays:
Apple M1:
Chipset Model: Apple M1
Type: GPU
Bus: Built-In
Total Number of Cores: 8
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2560 x 1600 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Usb Display: Va2055 Series (Usb):
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Usb Display: Lg Hdr Wfhd (Usb):
Resolution: 2560 x 1080 (UW-UXGA - Ultra Wide - Ultra Extended Graphics Array)
UI Looks like: 2560 x 1080 @ 60.00Hz
Mirror: Off
Online: Yes
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2021.5.30
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.36.2
ChimeraX-AtomicLibrary: 6.1.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.2
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4.dev202203190100
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.8
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.5
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.16.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.5.1
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.31.1
funcparserlib: 1.0.0a0
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.9.2
kiwisolver: 1.4.0
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.4
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.0
ParmEd: 3.4.3
parso: 0.8.3
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.28
psutil: 5.9.0
ptyprocess: 0.7.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.7
PyQt6-commercial: 6.2.3
PyQt6-sip: 13.2.0
PyQt6-WebEngine-commercial: 6.2.1
python-dateutil: 2.8.2
pytz: 2022.1
pyzmq: 22.3.0
qtconsole: 5.2.2
QtPy: 2.0.1
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Failed to lock QIOSurfaceGraphicsBuffer |
comment:2 by , 2 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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1.4; seems to be a crash in QWebEngine