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Opened 4 years ago
Closed 4 years ago
#6035 closed defect (can't reproduce)
OpenGL out of memory error, then crash several commands later on Windows
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | pett | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22000
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00001948 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006d74 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004e1c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006dd4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005f7c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002d84 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000064b0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000050c0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004a34 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005340 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003808 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00007654 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000051e0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002710 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004208 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000bd4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005ac8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005918 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004490 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000065d8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005ff4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002b14 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003490 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000773c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004ab0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00007674 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000036d4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b4c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006048 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001be8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006b14 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005744 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005e14 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001c50 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000a50 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000035cc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000043c0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005520 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006258 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006494 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006304 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000064c0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000376c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002fcc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000e60 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006d70 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005968 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001308 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000047f0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000034c0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000675c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002c94 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000434c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000039e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00007714 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000eac (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000595c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000064ec (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002884 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000004d0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004fb4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000076a8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000006c0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001140 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005814 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003744 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001748 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000077e4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003588 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004b5c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005f30 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005c9c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00004ae8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005f4c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006f34 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00001f70 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006dec (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00007628 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006a8c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000102c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000265c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00007008 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003948 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000031f8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005c74 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006f8c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000316c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005ac4 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000046d8 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00000f04 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 576 in _handle_results
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00007508 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 528 in _handle_tasks
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00002a04 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 816 in _exhaustive_wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\connection.py", line 884 in wait
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 499 in _wait_for_updates
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 519 in _handle_workers
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000064fc (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x0000719c (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005654 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00003eb0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x000010c0 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00006e48 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
Thread 0x00005750 (most recent call first):
File "C:\Program Files\ChimeraX 1.3\bin\lib\multiprocessing\pool.py", line 114 in worker
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 910 in run
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 973 in _bootstrap_inner
File "C:\Program Files\ChimeraX 1.3\bin\lib\threading.py", line 930 in _bootstrap
...
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "C:\Users\lilyh\Downloads\job866_VF_postprocess_5.06A (1).mrc" format
> mrc
Opened job866_VF_postprocess_5.06A (1).mrc as #1, grid size 400,400,400, pixel
1.05, shown at level 0.00336, step 2, values float32
> volume #1 step 1
> volume #1 level 0.01122
> volume #1 level 0.008029
> open "C:/Users/lilyh/Downloads/AF into EM version 3 (4).cxs"
Error opening map "C:\Users\lilyh\Downloads\AF into EM version 3 (4).cxs":
File AF into EM version 3 (4).cxs, format mrc
MRC header value nsymbt (1701082415) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Error opening map "C:\Users\lilyh\Downloads\AF into EM version 3 (4).cxs":
File AF into EM version 3 (4).cxs, format mrc
MRC header value nsymbt (1701082415) is invalid
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
opened ChimeraX session
> open "C:/Users/lilyh/Downloads/job862_Kinase_postprocess_6.7A (1).mrc"
Opened job862_Kinase_postprocess_6.7A (1).mrc as #1, grid size 400,400,400,
pixel 1.05, shown at level 0.00103, step 2, values float32
> open "C:/Users/lilyh/Downloads/job866_VF_postprocess_5.06A (1).mrc"
Opened job866_VF_postprocess_5.06A (1).mrc as #2, grid size 400,400,400, pixel
1.05, shown at level 0.00336, step 2, values float32
> hide #3.4 models
> show #3.4 models
> hide #3.1 models
> hide #3.2 models
> hide #3.3 models
> hide #3.4 models
> hide #3.5 models
> hide #!4 models
> hide #5 models
> hide #!2 models
> show #!2 models
> hide #!3 models
> hide #!1 models
> close #1
> volume #2 step 1
> volume #2 level 0.0118
> volume #2 level 0.01135
> volume gaussian #2 sdev2
Expected a keyword
> volume gaussian #2 sDev 2
Opened job866_VF_postprocess_5.06A (1).mrc gaussian as #1, grid size
400,400,400, pixel 1.05, shown at step 1, values float32
> volume #1 level 0.002588
> show #!2 models
> hide #!1 models
> show #!1 models
> hide #!2 models
> ui tool show AlphaFold
> close #2
> alphafold search #3.1
ChimeraX REST job id:
EEYTV4OQAHMC0V05OX5PY1GIU9CPC2LBHHGRU2XY6RBRXC1U0GT14D3IB7KP63T6
> alphafold search #3.1
ChimeraX REST job id:
HRCLWYDRNPBJY6SPIRQTW8QSUAYQ9GBDEY55Y8CDXTKHLCNSL2E0CXQAP8BAU26N
BlastProtein finished.
Parsing BLAST results.
> alphafold match #3.1
1 AlphaFold model found using UniProt identifier: Q08AM6 (chain A)
AlphaFold chains matching AF_hsVac14_pentamer.pdb
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | VAC14_HUMAN | Q08AM6 | 0.00 | 782 | 782 | 100
Opened 1 AlphaFold model
BlastProtein finished.
Parsing BLAST results.
> alphafold search #3.2
ChimeraX REST job id:
G32F5HWLS6Z8255U2HVK9QGJYEE9J56R25Y0ST6S1LGEVL07VK4YX1X8WZM3GV7O
> alphafold search #3.2
ChimeraX REST job id:
LL290JDJKBJHHF7CK2295O8JI36H4XMTU4BYMJFRGA35VOI0K6KAMG5290WHERM1
BlastProtein finished.
Parsing BLAST results.
BlastProtein finished.
Parsing BLAST results.
> alphafold fetch VAC14_YEAST alignTo #3.2/A
AlphaFold chains matching chain A
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | VAC14_YEAST | Q06708 | 7.20 | 871 | 782 | 34
> matchmaker #6 to #3.2/A
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 AF_hsVac14_pentamer.pdb, chain A (#3.2) with AlphaFold VAC14_YEAST,
chain A (#6), sequence alignment score = 1528.7
RMSD between 338 pruned atom pairs is 1.146 angstroms; (across all 657 pairs:
7.247)
> ui tool show AlphaFold
> hide #2.1 models
> show #2.1 models
> hide #2.1 models
> show #2.1 models
> close #2.1
> ui tool show AlphaFold
> show #3.1 models
> hide #3.1 models
> alphafold search #3.1
ChimeraX REST job id:
81T1OTFHUJPFJ9YA9CVMYHW5N3E4YQIKJ0W6WPK96H6OGTDB8X9JF7LDBM08SCD6
> alphafold search #3.1
ChimeraX REST job id:
M6GU5VD269WIIFIRC55PC6XQ5L1ZLXMG4WN53DBUQTMT9ND89MBF2PZYQFC7HIFB
BlastProtein finished.
Parsing BLAST results.
BlastProtein finished.
Parsing BLAST results.
> alphafold match #3.1
1 AlphaFold model found using UniProt identifier: Q08AM6 (chain A)
AlphaFold chains matching AF_hsVac14_pentamer.pdb
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | VAC14_HUMAN | Q08AM6 | 0.00 | 782 | 782 | 100
Opened 1 AlphaFold model
> alphafold fetch VAC14_YEAST alignTo #3.1/A
AlphaFold chains matching chain A
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | VAC14_YEAST | Q06708 | 7.20 | 871 | 782 | 34
> matchmaker #8 to #3.1/A
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 AF_hsVac14_pentamer.pdb, chain A (#3.1) with AlphaFold VAC14_YEAST,
chain A (#8), sequence alignment score = 1528.7
RMSD between 338 pruned atom pairs is 1.146 angstroms; (across all 657 pairs:
7.247)
> close #7.1
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> show #!4 models
> hide #!4 models
> alphafold search #4
ChimeraX REST job id:
3WDLDVD8RGSTGAUEV5X3AM03803HFUJ7XAJB532C8EKGFR5K5495VS9HZAX21YC1
> alphafold search #4
ChimeraX REST job id:
FPGR82IMZ8XHZIXQS4VJRBKO0BZJEWFXY973I43BEZYUKFAEMYKNB4G50TSJ1CTJ
BlastProtein finished.
Parsing BLAST results.
BlastProtein finished.
Parsing BLAST results.
> show #!4 models
> hide #!4 models
> alphafold fetch FAB1_YEAST alignTo #4/A
Fetching compressed AlphaFold P34756 from
https://alphafold.ebi.ac.uk/files/AF-P34756-F1-model_v1.cif
AlphaFold chains matching chain A
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | FAB1_YEAST | P34756 | 25.73 | 1698 | 1279 | 28
> matchmaker #9 to #4/A
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 Alphafold_domain_colored.pdb, chain A (#4) with AlphaFold
FAB1_YEAST, chain A (#9), sequence alignment score = 1869.8
RMSD between 460 pruned atom pairs is 1.185 angstroms; (across all 1171 pairs:
25.734)
> alphafold search #5
ChimeraX REST job id:
TEASL6PF0X4SZNNVLE7GIWAUABF5PX8F70S1IUVYE4JP9HPUIMEB18DTE2NX24K3
> alphafold search #5
ChimeraX REST job id:
NJBQAOJ8VZG11LRT6558HPEX3DQSRM40DEETOATQN2ZA8CSKWOG7UM27SLQFBRBY
> alphafold search #5
ChimeraX REST job id:
K85Y678G0BD8LA2JX35DLRKE1NU6R5TMZCUX8Q7QGVRO7V8GUNLFCRLYWCKRN8SW
BlastProtein finished.
Parsing BLAST results.
> close #1
BlastProtein finished.
Parsing BLAST results.
BlastProtein finished.
Parsing BLAST results.
> alphafold fetch FIG4_YEAST alignTo #5/A
Fetching compressed AlphaFold P42837 from
https://alphafold.ebi.ac.uk/files/AF-P42837-F1-model_v1.cif
AlphaFold chains matching chain A
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | FIG4_YEAST | P42837 | 29.33 | 865 | 907 | 38
> matchmaker #1 to #5/A
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 Alpha_fold_Fig4.pdb, chain A (#5) with AlphaFold FIG4_YEAST, chain
A (#1), sequence alignment score = 1724.7
RMSD between 512 pruned atom pairs is 0.821 angstroms; (across all 793 pairs:
29.327)
> ui tool show "Volume Viewer"
> close #1
> hide #!3 models
> show #!3 models
> hide #7 models
> show #7 models
> hide #8 models
> show #8 models
> show #!4 models
> hide #!4 models
> hide #2 models
> show #2 models
> hide #!3 models
> show #!3 models
> hide #2 models
> show #2 models
> open "C:/Users/lilyh/Downloads/job862_Kinase_postprocess_6.7A (1).mrc"
Opened job862_Kinase_postprocess_6.7A (1).mrc as #1, grid size 400,400,400,
pixel 1.05, shown at level 0.00103, step 2, values float32
> open "C:/Users/lilyh/Downloads/job866_VF_postprocess_5.06A (1).mrc"
Opened job866_VF_postprocess_5.06A (1).mrc as #10, grid size 400,400,400,
pixel 1.05, shown at level 0.00336, step 2, values float32
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!1 models
> show #!1 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #10 step 1
> volume #10 level 0.007419
> volume gaussian #10 sDev 2
Opened job866_VF_postprocess_5.06A (1).mrc gaussian as #11, grid size
400,400,400, pixel 1.05, shown at step 1, values float32
> volume #11 level 0.002197
> hide #6 models
> show #6 models
> hide #9 models
> show #9 models
> hide #9 models
> hide #8 models
> hide #!11 models
> show #!11 models
> hide #6 models
> show #6 models
> ui mousemode right "translate selected models"
Drag select of 5 residues
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> ui mousemode right select
> ui mousemode right translate
> select #6
6944 atoms, 7061 bonds, 871 residues, 1 model selected
> ~select #6
Nothing selected
> select #6
6944 atoms, 7061 bonds, 871 residues, 1 model selected
> ui mousemode right "translate selected models"
> hide #6 models
> show #6 models
> ~select #6
Nothing selected
> select #6
6944 atoms, 7061 bonds, 871 residues, 1 model selected
> hide #!11 models
> ui mousemode right select
> ui mousemode right "translate selected models"
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #6 models
> hide #7 models
> show #7 models
> show #6 models
> ui mousemode right select
> hide #!11 target m
> ui mousemode right "translate selected models"
> ui mousemode right translate
> ui mousemode right "move picked models"
> show #!11 models
> view matrix models
> #6,-0.21159,0.77628,0.59381,298.24,0.86772,0.42881,-0.25138,166.37,-0.44977,0.46207,-0.76432,385.15
> view matrix models
> #6,-0.21159,0.77628,0.59381,293.19,0.86772,0.42881,-0.25138,169.68,-0.44977,0.46207,-0.76432,377.06
> volume #11 level 0.004047
> volume #11 level 0.007747
> view matrix models
> #6,-0.21159,0.77628,0.59381,294.68,0.86772,0.42881,-0.25138,194.76,-0.44977,0.46207,-0.76432,293.76
> view matrix models #11,1,0,0,5.331,0,1,0,-0.67759,0,0,1,11.814
> view matrix models #11,1,0,0,8.4687,0,1,0,1.1294,0,0,1,21.46
> view matrix models #11,1,0,0,8.5854,0,1,0,-2.0235,0,0,1,17.271
> view matrix models
> #6,-0.21159,0.77628,0.59381,303.34,0.86772,0.42881,-0.25138,185.84,-0.44977,0.46207,-0.76432,296.75
> view matrix models
> #6,-0.21159,0.77628,0.59381,303.22,0.86772,0.42881,-0.25138,182.24,-0.44977,0.46207,-0.76432,309.07
> view matrix models
> #6,-0.21159,0.77628,0.59381,303.56,0.86772,0.42881,-0.25138,182.27,-0.44977,0.46207,-0.76432,309.55
> view matrix models
> #6,-0.21159,0.77628,0.59381,292.62,0.86772,0.42881,-0.25138,182.48,-0.44977,0.46207,-0.76432,295.16
> view matrix models
> #6,-0.21159,0.77628,0.59381,293.21,0.86772,0.42881,-0.25138,179.82,-0.44977,0.46207,-0.76432,293.02
> ui tool show "Fit in Map"
Fit molecule AlphaFold VAC14_YEAST (#6) to map job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) using 6944 atoms
average map value = 0.005491, steps = 140
shifted from previous position = 23.3
rotated from previous position = 0.807 degrees
atoms outside contour = 4575, contour level = 0.007747
Position of AlphaFold VAC14_YEAST (#6) relative to job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.21430801 0.76746845 0.60420548 267.83064670
0.86687911 0.43448951 -0.24441661 170.09255725
-0.45010298 0.47139267 -0.75841694 286.96897086
Axis 0.56000727 0.82482920 0.07777308
Axis point 133.69328583 0.00000000 115.14967302
Rotation angle (degrees) 140.27472700
Shift along axis 312.60287729
> show #8 models
> ~select #6
Nothing selected
> select #8
6944 atoms, 7061 bonds, 871 residues, 1 model selected
> view matrix models
> #8,-0.55035,0.53567,0.64045,254.9,0.34623,0.84442,-0.40876,169.55,-0.75977,-0.0032144,-0.65019,245.59
> view matrix models
> #8,-0.55035,0.53567,0.64045,252.18,0.34623,0.84442,-0.40876,172.28,-0.75977,-0.0032144,-0.65019,245.53
> view matrix models
> #8,-0.55035,0.53567,0.64045,252.37,0.34623,0.84442,-0.40876,171.45,-0.75977,-0.0032144,-0.65019,251.23
> view matrix models #11,1,0,0,27.938,0,1,0,3.5697,0,0,1,41.683
> view matrix models #11,1,0,0,26.814,0,1,0,4.1647,0,0,1,41.473
> view matrix models #11,1,0,0,34.197,0,1,0,6.6495,0,0,1,51.248
> view matrix models #11,1,0,0,9.2691,0,1,0,-1.4344,0,0,1,14.129
> view matrix models
> #8,-0.55035,0.53567,0.64045,251.97,0.34623,0.84442,-0.40876,171.73,-0.75977,-0.0032144,-0.65019,251.22
> view matrix models
> #8,-0.55035,0.53567,0.64045,245.35,0.34623,0.84442,-0.40876,161.82,-0.75977,-0.0032144,-0.65019,246.13
> view matrix models
> #8,-0.55035,0.53567,0.64045,246.63,0.34623,0.84442,-0.40876,163.87,-0.75977,-0.0032144,-0.65019,245.25
> view matrix models
> #8,-0.55035,0.53567,0.64045,246.63,0.34623,0.84442,-0.40876,163.02,-0.75977,-0.0032144,-0.65019,245
Fit molecule AlphaFold VAC14_YEAST (#8) to map job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) using 6944 atoms
average map value = 0.005715, steps = 68
shifted from previous position = 1.98
rotated from previous position = 1.11 degrees
atoms outside contour = 4609, contour level = 0.007747
Position of AlphaFold VAC14_YEAST (#8) relative to job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.54789186 0.53111740 0.64631943 237.72700904
0.32974655 0.84716282 -0.41663217 165.29505458
-0.76881839 -0.01514777 -0.63928775 229.08503023
Axis 0.27041321 0.95314280 -0.13563002
Axis point 154.86876254 0.00000000 82.89718290
Rotation angle (degrees) 132.06771271
Shift along axis 190.76350597
> show #!10 models
> hide #!10 models
> show #5 models
> hide #5 models
> show #!10 models
> hide #!10 models
> show #5 models
> hide #5 models
> ui tool show AlphaFold
> alphafold search #5
ChimeraX REST job id:
GIKVIOOEFQEXO3PP7PDRNDX9WZ1M1JKH7ZO66L9SKSO4Z6OJOUSZU6E92NLT2WA2
BlastProtein finished.
QWindowsWindow::setGeometry: Unable to set geometry 2256x1516+0+34 (frame:
2278x1572-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2256x1398+0+34 (frame: 2278x1454-11-11) margins: 11, 45,
11, 11 minimum size: 564x758 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1150,1572 maxtrack=0,0)
Parsing BLAST results.
QWindowsWindow::setGeometry: Unable to set geometry 2256x1748+0+34 (frame:
2278x1804-11-11) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 2256x1398+0+34 (frame: 2278x1454-11-11) margins: 11, 45,
11, 11 minimum size: 564x874 MINMAXINFO maxSize=0,0 maxpos=0,0
mintrack=1150,1804 maxtrack=0,0)
> alphafold fetch FIG4_YEAST alignTo #5/A
AlphaFold chains matching chain A
---
Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id
A | FIG4_YEAST | P42837 | 29.33 | 865 | 907 | 38
> matchmaker #12 to #5/A
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 Alpha_fold_Fig4.pdb, chain A (#5) with AlphaFold FIG4_YEAST, chain
A (#12), sequence alignment score = 1724.7
RMSD between 512 pruned atom pairs is 0.821 angstroms; (across all 793 pairs:
29.327)
> select clear
> hide #6 models
> hide #12 models
> show #12 models
> hide #8 models
> volume #11 level 0.01073
> volume #11 level 0.007804
> volume #11 level 0.006773
Drag select of 3 residues
> ui mousemode right select
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #!10 models
> hide #!10 models
> hide #12 models
> show #12 models
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.9933,0.10138,-0.055508,223.52,-0.11536,-0.89933,0.42179,196.32,-0.007157,0.42536,0.90499,272.56
> view matrix models
> #12,-0.9933,0.10138,-0.055508,220.08,-0.11536,-0.89933,0.42179,196.65,-0.007157,0.42536,0.90499,278.16
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.94943,0.010447,-0.31381,224.78,-0.12785,-0.92571,0.35598,197.42,-0.28678,0.37809,0.88023,273.45
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.94943,0.010447,-0.31381,220.75,-0.12785,-0.92571,0.35598,198.02,-0.28678,0.37809,0.88023,278.77
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.95282,-0.011709,-0.30331,220.62,-0.10954,-0.91865,0.37958,198.01,-0.28308,0.3949,0.87403,278.86
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #12,-0.97518,0.22113,-0.010927,215.34,-0.2043,-0.87973,0.42935,195.41,0.085332,0.42093,0.90307,285.26
> view matrix models
> #12,-0.95363,-0.18334,-0.23869,220.34,0.023843,-0.83658,0.54733,197.9,-0.30003,0.51626,0.80216,279.09
> view matrix models
> #12,-0.90923,-0.045544,-0.41379,223.08,-0.099231,-0.94163,0.32168,199.08,-0.40429,0.33354,0.85164,277.12
> view matrix models
> #12,-0.92528,-0.030474,-0.37806,222.23,-0.13664,-0.90306,0.40721,197.07,-0.35382,0.42844,0.83142,278
> view matrix models
> #12,-0.90955,-0.08779,-0.40623,223.12,-0.035779,-0.95727,0.28698,200.8,-0.41406,0.27556,0.86754,276.93
> view matrix models
> #12,-0.88905,0.059923,-0.45387,223.62,-0.24222,-0.90284,0.35526,195.81,-0.38849,0.42578,0.81718,277.56
> view matrix models
> #12,-0.87503,0.14639,-0.4614,223.68,-0.25109,-0.95218,0.17409,198.31,-0.41385,0.26818,0.86995,276.93
> view matrix models
> #12,-0.92946,0.055652,-0.36471,221.66,-0.18828,-0.92168,0.33919,197.1,-0.31727,0.38393,0.86714,278.35
> view matrix models
> #12,-0.94841,0.09883,-0.30124,220.28,-0.19405,-0.93236,0.30504,197.5,-0.25072,0.34776,0.90344,279.23
> view matrix models
> #12,-0.94933,0.10074,-0.29768,220.2,-0.19672,-0.92919,0.31289,197.33,-0.24509,0.3556,0.90193,279.33
> ui mousemode right "translate selected models"
> view matrix models
> #12,-0.94933,0.10074,-0.29768,217.62,-0.19672,-0.92919,0.31289,198.31,-0.24509,0.3556,0.90193,279.86
Fit molecule AlphaFold FIG4_YEAST (#12) to map job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) using 7077 atoms
average map value = 0.005856, steps = 276
shifted from previous position = 25.5
rotated from previous position = 16.2 degrees
atoms outside contour = 3914, contour level = 0.0067731
Position of AlphaFold FIG4_YEAST (#12) relative to job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.99520086 0.08947529 -0.03961597 228.42910668
-0.09782440 -0.89990208 0.42497839 193.70549892
0.00237457 0.42681427 0.90433619 279.00387751
Axis 0.00956397 -0.21874895 -0.97573430
Axis point 118.67192851 59.87389633 0.00000000
Rotation angle (degrees) 174.49233922
Shift along axis -312.42183870
> volume #11 level 0.006945
> show #!10 models
> hide #!10 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> select clear
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #!10 models
> hide #!10 models
> show #9 models
> hide #9 models
> show #9 models
> show #!10 models
> hide #!10 models
> hide #9 models
> show #9 models
> show #!4 models
> hide #!4 models
> show #!1 models
> volume #1 level 0.008162
> hide #!11 models
> show #!11 models
> volume #1 level 0.006814
> volume #1 level 0.005272
> volume #1 level 0.004887
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume #1 level 0.01192
> volume #1 level 0.007199
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.005176
> volume #1 level 0.008066
> ui mousemode right select
> select #9/A:1026
9 atoms, 8 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.86715,-0.249,0.43134,198.38,-0.12952,0.72351,0.67805,240.28,-0.48092,-0.64384,0.59514,185.11
> view matrix models
> #9,0.86346,0.14301,0.48371,196.91,-0.49691,0.076456,0.86443,234.77,0.086642,-0.98676,0.13708,198.4
> view matrix models
> #9,-0.25748,-0.25146,-0.93299,187.57,-0.9502,0.24133,0.19719,230.65,0.17557,0.9373,-0.30108,197.16
> view matrix models
> #9,-0.11805,-0.9673,-0.22449,187.68,-0.57262,-0.11838,0.81123,234.35,-0.81127,0.22431,-0.53992,183.91
> view matrix models
> #9,-0.10604,-0.9271,-0.3595,188.58,-0.64945,-0.2092,0.73106,233.79,-0.75298,0.311,-0.57992,184.89
> ui mousemode right "translate selected models"
> view matrix models
> #9,-0.10604,-0.9271,-0.3595,163.68,-0.64945,-0.2092,0.73106,248.58,-0.75298,0.311,-0.57992,249.92
> view matrix models
> #9,-0.10604,-0.9271,-0.3595,162.21,-0.64945,-0.2092,0.73106,245.41,-0.75298,0.311,-0.57992,259.8
> view matrix models
> #9,-0.10604,-0.9271,-0.3595,206.16,-0.64945,-0.2092,0.73106,216.07,-0.75298,0.311,-0.57992,149.86
> view matrix models
> #9,-0.10604,-0.9271,-0.3595,207.73,-0.64945,-0.2092,0.73106,213.83,-0.75298,0.311,-0.57992,154.8
> ui mousemode right "rotate selected models"
> view matrix models
> #9,-0.11417,-0.92547,-0.3612,207.6,-0.63212,-0.21281,0.74507,214.04,-0.76641,0.31339,-0.56072,154.45
> view matrix models
> #9,0.78455,-0.51279,0.3486,217.37,-0.5589,-0.34135,0.75572,215.58,-0.26853,-0.78774,-0.5544,165.9
> view matrix models
> #9,0.69548,-0.63015,0.34529,216.21,-0.44049,0.0057561,0.89774,215.76,-0.5677,-0.77645,-0.27357,159.13
> view matrix models
> #9,0.83426,-0.50317,0.22544,218.92,-0.25679,0.007248,0.96644,218.44,-0.48792,-0.86416,-0.12316,159.82
> view matrix models
> #9,0.86936,-0.20784,0.44835,217.35,-0.46894,-0.63318,0.61578,218.75,0.1559,-0.74558,-0.64792,173.51
> view matrix models
> #9,0.68006,-0.55483,0.47925,214.94,-0.30534,0.37996,0.87316,217.14,-0.66655,-0.74013,0.088983,155.19
> view matrix models
> #9,0.85553,0.49435,-0.1539,218.77,-0.33624,0.75652,0.56091,217.44,0.39371,-0.42813,0.81345,167.88
> view matrix models
> #9,0.93906,0.29531,-0.17597,220.87,-0.16277,0.83283,0.52905,220.35,0.30278,-0.46817,0.83015,166.36
> view matrix models
> #9,0.87383,0.34559,-0.34203,220.62,0.10795,0.54799,0.82949,223.91,0.4741,-0.76176,0.44154,172.4
> view matrix models
> #9,0.98722,0.1571,0.026584,220.85,-0.086533,0.38854,0.91736,220.55,0.13379,-0.90794,0.39717,167.33
> view matrix models
> #9,0.98524,0.17078,0.011701,220.87,-0.070228,0.34092,0.93747,220.84,0.15611,-0.92445,0.34788,168.05
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.98524,0.17078,0.011701,214.55,-0.070228,0.34092,0.93747,252.4,0.15611,-0.92445,0.34788,195.95
> view matrix models
> #9,0.98524,0.17078,0.011701,215.98,-0.070228,0.34092,0.93747,248.66,0.15611,-0.92445,0.34788,196.84
> view matrix models
> #9,0.98524,0.17078,0.011701,217.11,-0.070228,0.34092,0.93747,243.8,0.15611,-0.92445,0.34788,193.56
> view matrix models
> #9,0.98524,0.17078,0.011701,214.32,-0.070228,0.34092,0.93747,249.07,0.15611,-0.92445,0.34788,187.5
> view matrix models
> #9,0.98524,0.17078,0.011701,217.03,-0.070228,0.34092,0.93747,244.95,0.15611,-0.92445,0.34788,195.49
> view matrix models
> #9,0.98524,0.17078,0.011701,215.96,-0.070228,0.34092,0.93747,247.11,0.15611,-0.92445,0.34788,193.43
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.95691,0.16642,0.23798,214.13,-0.27412,0.24715,0.9294,243.98,0.095857,-0.95458,0.28212,192.89
> view matrix models
> #9,0.95477,0.22317,0.1965,214.19,-0.21753,0.073684,0.97327,245.15,0.20272,-0.97199,0.1189,195.72
> view matrix models
> #9,0.97735,0.1846,0.1035,215.23,-0.14621,0.23536,0.96085,245.98,0.15302,-0.95422,0.25702,194
> view matrix models
> #9,0.97572,-0.19264,0.10417,216.26,-0.049703,0.26847,0.962,247.51,-0.21329,-0.94383,0.25238,187.82
> view matrix models
> #9,0.98771,-0.14115,0.067081,216.54,-0.053323,0.099099,0.99365,247.74,-0.1469,-0.98502,0.090355,190.02
> view matrix models
> #9,0.9811,-0.073636,0.17892,215.57,-0.15201,0.27873,0.94826,245.84,-0.1197,-0.95754,0.26227,189.38
> view matrix models
> #9,0.9907,-0.011868,0.13556,215.82,-0.13419,0.080384,0.98769,246.46,-0.022619,-0.99669,0.078044,192.23
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
Fit molecule AlphaFold FAB1_YEAST (#9) to map job862_Kinase_postprocess_6.7A
(1).mrc (#1) using 13607 atoms
average map value = 0.003648, steps = 212
shifted from previous position = 17.8
rotated from previous position = 19.1 degrees
atoms outside contour = 10319, contour level = 0.008066
Position of AlphaFold FAB1_YEAST (#9) relative to
job862_Kinase_postprocess_6.7A (1).mrc (#1) coordinates:
Matrix rotation and translation
0.89270911 0.01315092 0.45044149 197.93009494
-0.45046926 0.05302122 0.89121617 235.30744014
-0.01216265 -0.99850681 0.05325661 196.90289384
Axis -0.94486158 0.23130209 -0.23181011
Axis point 0.00000000 224.17165919 -72.08961071
Rotation angle (degrees) 90.02902181
Shift along axis -178.23352185
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!11 models
> show #!11 models
> hide #!4 models
> show #8 models
> hide #8 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #8 models
> hide #8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:37
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:37-154
925 atoms, 939 bonds, 118 residues, 1 model selected
> select #6/A:10-17
72 atoms, 72 bonds, 8 residues, 1 model selected
> show #6 models
> select #6/A:75-76
12 atoms, 11 bonds, 2 residues, 1 model selected
> select #6/A:75-201
995 atoms, 1010 bonds, 127 residues, 1 model selected
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> select #6/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!11 models
> view matrix models
> #6,-0.64877,0.76097,-0.0057184,278.71,0.63474,0.53698,-0.55566,168.3,-0.41976,-0.36412,-0.83139,311.91
> show #!11 models
Fit molecule AlphaFold VAC14_YEAST (#6) to map job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) using 6944 atoms
average map value = 0.005491, steps = 408
shifted from previous position = 8.22
rotated from previous position = 49.8 degrees
atoms outside contour = 4172, contour level = 0.006945
Position of AlphaFold VAC14_YEAST (#6) relative to job866_VF_postprocess_5.06A
(1).mrc gaussian (#11) coordinates:
Matrix rotation and translation
-0.21659920 0.76814311 0.60252879 267.79415073
0.86583992 0.43626924 -0.24492935 170.07118000
-0.45100557 0.46864198 -0.75958454 286.96542047
Axis 0.55914150 0.82553035 0.07655344
Axis point 133.74431916 0.00000000 115.22805955
Rotation angle (degrees) 140.35004968
Shift along axis 312.10193260
> select #6/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!11 models
> ui mousemode right translate
> ui mousemode right zoom
> ui mousemode right "translate selected models"
> select #6/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> ui tool show Contacts
> contacts sel resSeparation 3
133 contacts
> contacts sel resSeparation 3
133 contacts
> contacts sel resSeparation 3
133 contacts
> hide #13 models
> show #13 models
> hide #12 models
> show #12 models
> show sel atoms
Drag select of 1 residues
> show sel atoms
> select clear
Drag select of 2 atoms, 1 residues
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
Drag select of 1 residues
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #12 models
> show #12 models
> ui tool show Contacts
> show #!11 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> select #6/A:10-11
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #6/A:10-18
81 atoms, 81 bonds, 9 residues, 1 model selected
> select clear
> select #6/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #8 models
> ui tool show "Show Sequence Viewer"
> hide #6 models
> show #6 models
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> show #!11 models
> hide #!11 models
> select #8/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:59-60
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #8/A:59-60
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #8/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide #12 models
> show #12 models
> hide #12 models
> select #8/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #8/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel magenta
> show sel atoms
> select #8/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #8/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #8/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select clear
> select #8/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/A:149
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel white
> show sel atoms
Drag select of 1 atoms, 2 residues
> select clear
Drag select of 1 atoms, 2 residues
> select clear
Drag select of 1 atoms, 2 residues
> color sel white
> select clear
> show #12 models
> hide #12 models
> show #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
> select #12/A:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #6 models
> show #6 models
> hide #12 models
> select #12/A:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:65
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #12/A:66-67
13 atoms, 12 bonds, 2 residues, 1 model selected
> select #12/A:66-68
21 atoms, 20 bonds, 3 residues, 1 model selected
> select #12/A:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> select #12/A:66
4 atoms, 3 bonds, 1 residue, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select #8/A:39-40
19 atoms, 18 bonds, 2 residues, 1 model selected
> select #8/A:39-119
627 atoms, 637 bonds, 81 residues, 1 model selected
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select clear
> select #6/A:10-37
226 atoms, 227 bonds, 28 residues, 1 model selected
> select #6/A:10-111
805 atoms, 817 bonds, 102 residues, 1 model selected
> select clear
> select #6/A:10-85
597 atoms, 603 bonds, 76 residues, 1 model selected
> select #6/A:53
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #6/A:53-129
599 atoms, 611 bonds, 77 residues, 1 model selected
> select clear
> select
> #6/A:14-34,37-52,58-96,100-135,141-161,176-178,204-214,220-235,241-256,261-305,317-329,363-366,379-380,390-400,406-422,424-441,447-466,478-488,494-510,512-515,519-530,535-548,554-570,572-589,592-603,609-625,627-638,642-652,656-665,669-679,686-698,702-710,718-730,735-751,754-761,781-783,785-812
4596 atoms, 4643 bonds, 4 pseudobonds, 566 residues, 2 models selected
> select clear
> select #6/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:56
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #6/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #6/A:61
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select #6/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> select #6/A:101
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel magenta
> select clear
> show #12 models
> hide #13 models
> show #13 models
Drag select of 8 atoms, 10 residues, 7 bonds
Drag select of 5 atoms, 5 bonds, 25 residues
> show sel atoms
> select clear
Drag select of 24 atoms, 8 residues, 23 bonds
> ui tool show Contacts
> contacts sel resSeparation 3
942 contacts
> select clear
Drag select of 1 residues
> hide #8 models
> show #8 models
> ui tool show "Show Sequence Viewer"
> sequence chain #8/A
Alignment identifier is 8/A
> select clear
Drag select of 1 residues
> select clear
> hide #6 models
> show #6 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> show #9 models
> hide #6 models
> show #6 models
> hide #12 models
> show #12 models
> show #!11 models
> hide #!11 models
> hide #12 models
> show #12 models
> ui tool show "Show Sequence Viewer"
> sequence chain #12/A
Alignment identifier is 12/A
Drag select of 1 residues
> select #12/A:596
12 atoms, 12 bonds, 1 residue, 1 model selected
> select #12/A:596
12 atoms, 12 bonds, 1 residue, 1 model selected
> select clear
Drag select of 1 atoms, 1 residues
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> open 6KYB
Summary of feedback from opening 6KYB fetched from pdb
---
note | Fetching compressed mmCIF 6kyb from
http://files.rcsb.org/download/6kyb.cif
6kyb title:
Crystal structure of Atg18 from Saccharomyces cerevisiae [more info...]
Chain information for 6kyb #14
---
Chain | Description | UniProt
A B C D | Autophagy-related protein 18 | ATG18_YEAST
6kyb mmCIF Assemblies
---
1| author_defined_assembly
2| author_defined_assembly
3| author_defined_assembly
4| author_defined_assembly
Drag select of 82 residues
> view matrix models #14,1,0,0,94.325,0,1,0,158.86,0,0,1,464.73
> select clear
Drag select of 78 residues, 1 pseudobonds
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,120.02,0,1,0,16.761,0,0,1,170.21
> view matrix models #14,1,0,0,122.69,0,1,0,18.229,0,0,1,185.13
> view matrix models #14,1,0,0,185.92,0,1,0,14.143,0,0,1,429.82
> view matrix models #14,1,0,0,192.89,0,1,0,-0.74462,0,0,1,416.31
> view matrix models #14,1,0,0,76.075,0,1,0,188.16,0,0,1,392.49
> ui mousemode right "move picked models"
> view matrix models #14,1,0,0,120.72,0,1,0,35.94,0,0,1,193.64
> ui mousemode right select
Drag select of 6 residues
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
> view matrix models #14,1,0,0,131.5,0,1,0,51.827,0,0,1,223.7
> ui tool show "Show Sequence Viewer"
> sequence chain #14/A
Alignment identifier is 14/A
> select #14/A:32-33
14 atoms, 13 bonds, 2 residues, 1 model selected
> select #14/A:32-147
908 atoms, 925 bonds, 116 residues, 1 model selected
> select #14/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #14/A:87
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel magenta
> show sel atoms
> select #14/A:73
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #14/A:73-74
22 atoms, 21 bonds, 2 residues, 1 model selected
> select clear
> show #!11 models
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #3.1 models
> hide #3.1 models
> show #!4 models
> hide #!4 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
Drag select of 28 residues, 11 job866_VF_postprocess_5.06A (1).mrc gaussian
Drag select of 37 residues
> show sel atoms
> hide sel atoms
> select clear
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> select #10
2 models selected
> ui mousemode right "translate selected models"
> view matrix models #10,1,0,0,6.2398,0,1,0,-5.6027,0,0,1,16.337
> view matrix models #10,1,0,0,3.6159,0,1,0,9.7928,0,0,1,27.083
> view matrix models #10,1,0,0,2.579,0,1,0,19.963,0,0,1,36.849
> view matrix models #10,1,0,0,-15.084,0,1,0,45.434,0,0,1,3.5876
> volume #10 level 0.01271
> view matrix models #10,1,0,0,5.233,0,1,0,-3.3733,0,0,1,15.492
> show #5 models
> hide #5 models
> show #5 models
> hide #5 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> volume #11 level 0.004883
> volume #11 level 0.002362
> show #!1 models
> ui tool show "Show Sequence Viewer"
> sequence chain #9/A
Alignment identifier is 9/A
> select #9/A:2250
7 atoms, 6 bonds, 1 residue, 1 model selected
> select #9/A:2250
7 atoms, 6 bonds, 1 residue, 1 model selected
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> show sel atoms
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select
> #9/A:672-679,704-710,790-805,812-826,829-831,841-845,856-858,904-924,938-945,957-967,969-970,975-979,1012-1014,1025-1054,1061-1073,1081-1088,1100-1125,1131-1136,1142-1144,1150-1181,1189-1191,1228-1238,1251-1253,1277-1279,1296-1298,1301-1306,1310-1319,1322-1324,1328-1330,1364-1366,1369-1370,1373-1402,1412-1446,1453-1480,1484-1498,1648-1681,1684-1687,1700-1704,1706-1708,1752-1754,1823-1835,1839-1845,1861-1862,1869-1877,1879-1899,1970-1985,2011-2020,2024-2031,2063-2085,2093-2094,2156-2165,2172-2191,2223-2233,2251-2265,2270
5006 atoms, 5055 bonds, 600 residues, 1 model selected
> select #9/A:2257
11 atoms, 10 bonds, 1 residue, 1 model selected
> select #9/A:2257
11 atoms, 10 bonds, 1 residue, 1 model selected
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> volume #11 level 0.001216
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.
GLError(
err = 1285,
description = b'out of memory',
baseOperation = glBufferData,
pyArgs = (
34963,
133719744,
array([[ 0, 2, 5],
[ 0, 4, 2],
[ 3, 0, 5],
.....,
GL_STATIC_DRAW,
),
cArgs = (
34963,
133719744,
array([[ 0, 2, 5],
[ 0, 4, 2],
[ 3, 0, 5],
.....,
GL_STATIC_DRAW,
),
cArguments = (
34963,
133719744,
array([[ 0, 2, 5],
[ 0, 4, 2],
[ 3, 0, 5],
.....,
GL_STATIC_DRAW,
)
)
Traceback (most recent call last):
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\updateloop.py", line 73, in draw_new_frame
view.draw(check_for_changes = False)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\view.py", line 165, in draw
self._draw_scene(camera, drawings)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\view.py", line 235, in _draw_scene
draw_opaque(r, opaque_drawings)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1499, in draw_opaque
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1512, in _draw_multiple
d.draw(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 752, in draw
self.draw_self(renderer, draw_pass)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 759, in draw_self
self._draw_geometry(renderer, opaque_only = any_transp)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 786, in _draw_geometry
ds.activate_bindings(renderer)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1859, in activate_bindings
self.update_buffers()
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\drawing.py", line 1847, in update_buffers
b.update_buffer_data(data)
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\graphics\opengl.py", line 2674, in update_buffer_data
GL.glBufferData(btype, size, d, GL.GL_STATIC_DRAW)
File "src/latebind.pyx", line 51, in OpenGL_accelerate.latebind.Curry.__call__
File "C:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\OpenGL\GL\VERSION\GL_1_5.py", line 89, in glBufferData
return baseOperation( target, size, data, usage )
File "src/latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__
File "src/wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__
File "src/errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError
OpenGL.error.GLError: GLError(
err = 1285,
description = b'out of memory',
baseOperation = glBufferData,
pyArgs = (
34963,
133719744,
array([[ 0, 2, 5],
[ 0, 4, 2],
[ 3, 0, 5],
.....,
GL_STATIC_DRAW,
),
cArgs = (
34963,
133719744,
array([[ 0, 2, 5],
[ 0, 4, 2],
[ 3, 0, 5],
.....,
GL_STATIC_DRAW,
),
cArguments = (
34963,
133719744,
array([[ 0, 2, 5],
[ 0, 4, 2],
[ 3, 0, 5],
.....,
GL_STATIC_DRAW,
)
)
> volume #11 level -0.0009031
> volume #11 level -0.001533
> volume #11 level 0.002534
> volume #11 level -0.002851
> volume #11 level -0.001361
> volume #11 level 0.004654
> volume #11 level 0.002419
> volume #11 level 0.0109
> show #!4 models
> hide #!4 models
> hide #!14 models
> show #!14 models
> hide #!11 models
> show #!11 models
===== Log before crash end =====
Log:
UCSF ChimeraX version: 1.3 (2021-12-08)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.14756 Core Profile Forward-Compatible Context 20.40.53.01 27.20.14053.1000
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Microsoft Corporation
Model: Surface Laptop 4
OS: Microsoft Windows 11 Home (Build 22000)
Memory: 8,002,093,056
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 Microsoft Surface (R) Edition
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.10.8
cftime: 1.5.1.1
charset-normalizer: 2.0.9
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
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
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3
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-DistUI: 1.0
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: 1.1.4
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: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
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: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
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: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.7
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
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
comtypes: 1.1.10
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.8.0
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.3
ParmEd: 3.2.0
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pywin32: 228
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.3
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
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-jurko: 0.6
tables: 3.6.1
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Unknown crash |
comment:2 by , 4 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
| Summary: | Unknown crash → OpenGL out of memory error, then crash several commands later on Windows |
This error "Fatal Python error: Aborted" is not the usual "access violation" and my hypothesis is that the "Aborted" errors mean Qt called abort() maybe due to lack of resources.
There was an OpenGL out of memory error several commands before the crash trying to allocate 130 Mbytes of triangle data for a volume that had a low contour level just set
GLError( err = 1285, description = b'out of memory', baseOperation = glBufferData, pyArgs = ( 34963, 133719744, array([[ 0, 2, 5], ...
This was with AMD Radeon graphics and I am not sure if the out of memory was with graphics memory (most likely) or CPU memory (possible). It could be related to the subsequent crash -- something may have run out of memory after a few more volume level changes and hiding a few models causing some code to detect a memory allocation failure and call abort(). Or maybe even a graphics driver crash might call abort() on Windows -- don't know.
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It was well after there was an out-of-memory error on the graphics card.