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Opened 3 years ago
Closed 3 years ago
#7740 closed defect (can't reproduce)
Crash in event loop after session opened
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-48-generic-x86_64-with-glibc2.31
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: Segmentation fault
Thread 0x00007fddffbff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcdf7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcdffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcfcff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py", line 936 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcfd7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcfdffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcfe7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcfeffd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcff7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdcfffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd1ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd3ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd5ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdd7ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda0ff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda17fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda1ffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda27fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda2ffd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda37fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdda3fff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdde8ff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdde97fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fdde9ffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fddea7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fddeaffd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fddeb7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Thread 0x00007fddebfff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap
Current thread 0x00007fdeb21d6740 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== 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 /alphafold-
> libs/otter/shared/mat/hftv-1/220518_Bristol/Refine3D/job811/run_class001.mrc
Opened run_class001.mrc as #1, grid size 512,512,512, pixel 1.35, shown at
level 0.0137, step 2, values float32
> volume #1 step 1
> volume #1 level 0.008989
> volume #1 level 0.00416
> volume #1 level 0.002594
> volume #1 level 0.003769
> ui mousemode right "map eraser"
> volume erase #1 center 372.38,203.13,7.4745 radius 351.99
Opened run_class001.mrc copy as #3, grid size 512,512,512, pixel 1.35, shown
at step 1, values float32
> volume erase #3 center 250.81,299.08,364.87 radius 91.238 outside true
> volume erase #3 center 191.97,267.31,301.83 radius 43.891
> volume erase #3 center 245.15,213.22,332.48 radius 43.891
> volume erase #3 center 327.87,223.9,359.39 radius 43.891
> volume erase #3 center 332.39,252.42,365.41 radius 29.03
> volume erase #3 center 223.58,338.43,296.01 radius 29.722
> volume erase #3 center 313.6,366.82,372.86 radius 29.722
> save /usr/local/model-angelo/hftv_turret/hftv_turret_small.mrc models #3
Cannot save '/usr/local/model-angelo/hftv_turret/hftv_turret_small.mrc':
[Errno 13] Permission denied: '/usr/local/model-
angelo/hftv_turret/hftv_turret_small.mrc'
> save /home/alphafold/Desktop/turret_small.mrc models #3
> close #3
> open /usr/local/model-angelo/hftv_turret_single/turret_small_fixed.mrc
Opened turret_small_fixed.mrc as #2, grid size 460,460,460, pixel 1.5, shown
at level 1.67e-05, step 2, values float32
> volume #2 step 1
> volume #2 level 0.005037
> volume #2 level 0.005468
> volume #2 level 0.01508
> volume #2 level 0.01178
> volume #2 level 0.001881
> volume #2 level 0.01809
> volume #2 level 0.003603
> volume #2 level 0.002312
> volume #2 level 0.003029
> volume #2 level 0.01809
> volume threshold #2 minimum 0.003 set 0 maximum 0.0181 setMaximum 0
Opened turret_small_fixed.mrc thresholded as #3, grid size 460,460,460, pixel
1.5, shown at step 1, values float32
> volume #3 level 0.004582
Must specify 6 comma-separated integers, got #2
> ui mousemode right "mark surface"
> marker #4 position 207.1,269.7,397.4 color yellow radius 1
> marker #4 position 261.9,333.7,404.5 color yellow radius 1
> select /M:1@M
1 atom, 1 residue, 1 model selected
> select add /M:2@M
2 atoms, 2 residues, 1 model selected
> distance sel
Distance between /M mark 1 M and mark 2 M: 84.609Å
> open /home/alphafold/Desktop/turret_small_box200.mrc
Opened turret_small_box200.mrc as #6, grid size 200,200,200, pixel 1.35, shown
at level 0.00298, step 1, values float32
> volume #6 level 0.003978
> marker #4 position 30.19,113.5,143 color yellow radius 1
> ui mousemode right "translate selected models"
> select #6
2 models selected
> view matrix models #6,1,0,0,263.3,0,1,0,87.809,0,0,1,229.52
> vop origin #6
Must specify float or 3 comma-separated floats, got #6
> open /home/alphafold/Desktop/turret_small.mrc
Opened turret_small.mrc as #7, grid size 512,512,512, pixel 1.35, shown at
level 4.88e-07, step 2, values float32
> volume #7 level 0.004481
> volume #7 step 1
> volume #7 level 0.002934
> open /usr/local/model-angelo/hftv_turret/run_class001_fixed.mrc
Opened run_class001_fixed.mrc as #8, grid size 460,460,460, pixel 1.5, shown
at level 0.0189, step 2, values float32
> volume #7 level 0.001275
> volume #8 level -0.001046
> close #8
> volume #6 level -0.0002235
Must specify float or 3 comma-separated floats, got #2
Must specify float or 3 comma-separated floats, got #2
> view matrix models #6,1,0,0,263,0,1,0,87.787,0,0,1,228.93
> close #6
> close #7
> close #2
> close #3
> open /usr/local/model-angelo/hftv_turret/turret_small.mrc
Opened turret_small.mrc as #2, grid size 512,512,512, pixel 1.35, shown at
level 4.88e-07, step 2, values float32
> measure center #2
Center of mass grid index for turret_small.mrc = (196.55, 228.66, 270.05)
> vop origin #2 196.55, 228.66, 270.05
Must specify float or 3 comma-separated floats, got #2
> vop origin #2 196.55,228.66,270.05
Must specify float or 3 comma-separated floats, got #2
Must specify float or 3 comma-separated floats, got #2
> volume #2 originIndex 196.55,228.66,270.05
> volume #2 level 0.001788
> volume #2 level 0.001192
> save /home/alphafold/Desktop/turret_small_centred.mrc models #2
> open /usr/local/model-angelo/hftv_turret_single/hftv_turret_single.cif
Summary of feedback from opening /usr/local/model-
angelo/hftv_turret_single/hftv_turret_single.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for hftv_turret_single.cif #3
---
Chain | Description
3 | No description available
6 AM | No description available
8 | No description available
9 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AD AG | No description available
AE | No description available
AH | No description available
AL | No description available
AN | No description available
AO | No description available
AV | No description available
Ai | No description available
Ap | No description available
Az | No description available
B | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
BN | No description available
BO | No description available
BP | No description available
BQ | No description available
BR | No description available
BS | No description available
BT | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
BZ | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
Bj | No description available
Bk | No description available
Bl | No description available
Bm | No description available
Bn | No description available
Bo | No description available
Bp | No description available
Bq | No description available
Br | No description available
Bs | No description available
Bt | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
d | No description available
e | No description available
f | No description available
g | No description available
h | No description available
j | No description available
q | No description available
w | No description available
x | No description available
y | No description available
z | No description available
> hide atoms
> hide cartoons
> show cartoons
> volume #2 step 1
> volume #2 level 0.003994
> volume #2 level 0.006904
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #3 models
> show #3 models
> close #2
> open /usr/local/model-angelo/hftv_turret_single/turret_small_box200.mrc
Opened turret_small_box200.mrc as #2, grid size 200,200,200, pixel 1.35, shown
at level 0.00298, step 1, values float32
> close #2
> open /usr/local/model-angelo/hftv_turret_single/turret_small_box200.mrc
Opened turret_small_box200.mrc as #2, grid size 200,200,200, pixel 1.35, shown
at level 0.00298, step 1, values float32
> open /usr/local/model-angelo/hftv_turret_single/turret_small_fixed.mrc
Opened turret_small_fixed.mrc as #6, grid size 460,460,460, pixel 1.5, shown
at level 1.67e-05, step 2, values float32
> close #6
> open /home/alphafold/Desktop/turret_small.mrc
> /home/alphafold/Desktop/turret_small_centred.mrc
> /home/alphafold/Desktop/turret_small_box200.mrc
Opened turret_small.mrc as #6.1, grid size 512,512,512, pixel 1.35, shown at
level 4.88e-07, step 2, values float32
Opened turret_small_centred.mrc as #6.2, grid size 512,512,512, pixel 1.35,
shown at level 4.88e-07, step 2, values float32
Opened turret_small_box200.mrc as #6.3, grid size 200,200,200, pixel 1.35,
shown at level 0.00298, step 1, values float32
> hide #3 models
> show #3 models
> close #6.3
> volume #6.1 originIndex 196.55,228.66,270.05
> volume #6.1 step 1
> volume #6.1 level 0.002212
> save /home/alphafold/Desktop/turret_small_centred.mrc models #6.1
> open /home/alphafold/Desktop/turret_small_centred.mrc
Opened turret_small_centred.mrc as #7, grid size 512,512,512, pixel 1.35,
shown at level 4.88e-07, step 2, values float32
> volume #7 step 1
> volume #7 level 0.001438
> open /home/alphafold/Desktop/turret_small_box200_centred.mrc
Opened turret_small_box200_centred.mrc as #8, grid size 200,200,200, pixel
1.35, shown at level 0.00298, step 1, values float32
> close #8
> volume #6.2 level 0.004481
> close #7
> close #6.2
> close #6.1
> close #2
> open /home/alphafold/Desktop/turret_small_box200_centred.mrc
Opened turret_small_box200_centred.mrc as #2, grid size 200,200,200, pixel
1.35, shown at level 0.00298, step 1, values float32
> close #2
> open /home/alphafold/Desktop/turret_small.mrc
> /home/alphafold/Desktop/turret_small_box200_centred.mrc
Opened turret_small.mrc as #2.1, grid size 512,512,512, pixel 1.35, shown at
level 4.88e-07, step 2, values float32
Opened turret_small_box200_centred.mrc as #2.2, grid size 200,200,200, pixel
1.35, shown at level 0.00298, step 1, values float32
> vop #2.1 onGrid #2.2
> volume #2.1 onGrid #2.2
Expected a keyword
> vop origin #2 196.55,228.66,270.05
Must specify float or 3 comma-separated floats, got #2
> vop #2 origin 196.55,228.66,270.05
> volume #2.1 level 0.0005962
> volume #2.1 step 1
> save /home/alphafold/Desktop/turret_small_centred.mrc models #2.1
> close #2.1
> open /home/alphafold/Desktop/turret_small_centred.mrc
Opened turret_small_centred.mrc as #7, grid size 512,512,512, pixel 1.35,
shown at level 4.88e-07, step 2, values float32
> volume #2.2 level 0.001582
> volume #7 level 4.878e-07
> volume #7 level 0.0003976
> open /home/alphafold/Desktop/turret_small_box200.mrc
Opened turret_small_box200.mrc as #8, grid size 200,200,200, pixel 1.35, shown
at level 0.00298, step 1, values float32
> close #8
> close #7
> close #2.2
> open /home/alphafold/Desktop/turret_small_box200.mrc
Opened turret_small_box200.mrc as #7, grid size 200,200,200, pixel 1.35, shown
at level 0.00298, step 1, values float32
> volume #7 level 0.001582
> open /home/alphafold/Desktop/turret_small_centred.mrc
Opened turret_small_centred.mrc as #8, grid size 512,512,512, pixel 1.35,
shown at level 4.88e-07, step 2, values float32
> volume #8 step 1
> volume #8 level 0.000755
> volume #7 level 0.00115
> volume #!7 region all imageMode "full region"
> volume unzone #!7
> mousemode rightMode "crop volume"
> volume #8 level -0.0004307
> volume #8 region 49,0,0,511,511,511
> volume #8 region 139,0,0,511,511,511
> volume #8 region 100,0,0,511,511,511
> volume #8 region 100,0,0,329,511,511
> volume #8 region 100,0,0,329,299,511
> volume #8 region 100,0,0,329,299,349
> volume #8 region 100,0,150,329,299,349
> volume #8 region 100,100,150,329,299,349
> volume #8 region 100,100,150,301,299,349
> volume #8 region 100,100,150,299,299,349
> volume #8 level 0.004096
> volume #8 level 0.0003238
> volume #8 level 0.002695
> save /home/alphafold/Desktop/turret_small_box200_centred.mrc models #8
> volume #8 level -0.0003229
> volume #!8 region all imageMode "full region"
> volume unzone #!8
> mousemode rightMode "crop volume"
> volume #8 region 0,0,0,511,398,511
> volume #8 region 49,0,0,511,398,511
> volume #8 level 0.0004209
> hide target m
> open /usr/local/model-
> angelo/hftv_turret_single_centred/turret_small_box200_centred.mrc
Opened turret_small_box200_centred.mrc as #9, grid size 200,200,200, pixel
1.35, shown at level 0.00308, step 1, values float32
> open /usr/local/model-
> angelo/hftv_turret_single_centred/turret_small_box200_centred_fixed.mrc
Opened turret_small_box200_centred_fixed.mrc as #10, grid size 180,180,180,
pixel 1.5, shown at level 0.00426, step 1, values float32
> volume #10 level 0.01275
> open /usr/local/model-
> angelo/hftv_turret_single_centred/hftv_turret_single_centred.cif
Summary of feedback from opening /usr/local/model-
angelo/hftv_turret_single_centred/hftv_turret_single_centred.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Chain information for hftv_turret_single_centred.cif #11
---
Chain | Description
2 | No description available
3 | No description available
5 d | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AH | No description available
AJ | No description available
AO | No description available
AP | No description available
Aa l | No description available
Af | No description available
At | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
BN | No description available
BO | No description available
BP | No description available
BQ | No description available
BR | No description available
BS | No description available
BT | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
BZ | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X y | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
m | No description available
r | No description available
t | No description available
u | No description available
w | No description available
> open /usr/local/model-
> angelo/hftv_turret_single_centred/turret_small_box200_centred.mrc
Opened turret_small_box200_centred.mrc as #12, grid size 200,200,200, pixel
1.35, shown at level 0.00308, step 1, values float32
> volume #12 level 0.001597
> volume #12 level 0.004147
> volume #12 level 0.007548
> select #12
2 models selected
> volume #12 region 0,0,0,199,199,199
> undo
> ui mousemode right "translate selected models"
> select #12
2 models selected
> view matrix models #12,1,0,0,-333.61,0,1,0,-353.91,0,0,1,-497.29
> view matrix models #12,1,0,0,-343.77,0,1,0,-366.91,0,0,1,-485.13
> view matrix models #12,1,0,0,-336.88,0,1,0,-365.71,0,0,1,-472.68
> view matrix models #12,1,0,0,-335.04,0,1,0,-362.51,0,0,1,-471.67
> view matrix models #12,1,0,0,-334.51,0,1,0,-365.08,0,0,1,-471.73
> view matrix models #12,1,0,0,-332.88,0,1,0,-363.59,0,0,1,-472.22
> ui tool show "Fit in Map"
Fit molecule hftv_turret_single_centred.cif (#11) to map
turret_small_box200_centred.mrc (#12) using 10810 atoms
average map value = 0.01085, steps = 48
shifted from previous position = 1.37
rotated from previous position = 0.0151 degrees
atoms outside contour = 3795, contour level = 0.0075477
Position of hftv_turret_single_centred.cif (#11) relative to
turret_small_box200_centred.mrc (#12) coordinates:
Matrix rotation and translation
0.99999998 0.00017078 -0.00013870 331.53608172
-0.00017076 0.99999997 0.00014437 363.65022075
0.00013872 -0.00014435 0.99999998 472.54008782
Axis -0.54861316 -0.52713222 -0.64896473
Axis point 29681.73611334 243897.84713912 0.00000000
Rotation angle (degrees) 0.01507681
Shift along axis -680.23865725
> select clear
> volume #12 level 0.002777
> close #12
> close
> open /usr/local/model-
> angelo/hftv_turret_single_centred/turret_small_box200_centred.mrc
> /usr/local/model-
> angelo/hftv_turret_single_centred/hftv_turret_single_centred.cif
Summary of feedback from opening /usr/local/model-
angelo/hftv_turret_single_centred/hftv_turret_single_centred.cif
---
warnings | Missing entity information. Treating each chain as a separate
entity.
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.
Opened turret_small_box200_centred.mrc as #1, grid size 200,200,200, pixel
1.35, shown at level 0.00308, step 1, values float32
Chain information for hftv_turret_single_centred.cif #2
---
Chain | Description
2 | No description available
3 | No description available
5 d | No description available
6 | No description available
7 | No description available
8 | No description available
A | No description available
A0 | No description available
A1 | No description available
A2 | No description available
A3 | No description available
A4 | No description available
A5 | No description available
A6 | No description available
A7 | No description available
A8 | No description available
A9 | No description available
AA | No description available
AH | No description available
AJ | No description available
AO | No description available
AP | No description available
Aa l | No description available
Af | No description available
At | No description available
Av | No description available
Aw | No description available
Ax | No description available
Ay | No description available
Az | No description available
B | No description available
BA | No description available
BB | No description available
BC | No description available
BD | No description available
BE | No description available
BF | No description available
BG | No description available
BH | No description available
BI | No description available
BJ | No description available
BK | No description available
BL | No description available
BM | No description available
BN | No description available
BO | No description available
BP | No description available
BQ | No description available
BR | No description available
BS | No description available
BT | No description available
BU | No description available
BV | No description available
BW | No description available
BX | No description available
BY | No description available
BZ | No description available
Ba | No description available
Bb | No description available
Bc | No description available
Bd | No description available
Be | No description available
Bf | No description available
Bg | No description available
Bh | No description available
Bi | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
J | No description available
K | No description available
L | No description available
M | No description available
N | No description available
O | No description available
P | No description available
Q | No description available
R | No description available
S | No description available
T | No description available
U | No description available
V | No description available
W | No description available
X y | No description available
Y | No description available
Z | No description available
a | No description available
b | No description available
c | No description available
g | No description available
h | No description available
i | No description available
j | No description available
k | No description available
m | No description available
r | No description available
t | No description available
u | No description available
w | No description available
> select #2
10810 atoms, 10816 bonds, 1509 residues, 1 model selected
> view matrix models #2,1,0,0,317.99,0,1,0,201.98,0,0,1,515.09
> view matrix models #2,1,0,0,374.93,0,1,0,321.92,0,0,1,469.1
> view matrix models #2,1,0,0,337.34,0,1,0,363.8,0,0,1,470.95
> view matrix models #2,1,0,0,333.9,0,1,0,361.47,0,0,1,472.7
Fit molecule hftv_turret_single_centred.cif (#2) to map
turret_small_box200_centred.mrc (#1) using 10810 atoms
average map value = 0.01085, steps = 52
shifted from previous position = 3.22
rotated from previous position = 0.0215 degrees
atoms outside contour = 933, contour level = 0.0030849
Position of hftv_turret_single_centred.cif (#2) relative to
turret_small_box200_centred.mrc (#1) coordinates:
Matrix rotation and translation
0.99999993 0.00029850 -0.00020251 331.52435804
-0.00029848 0.99999995 0.00010053 363.69035290
0.00020254 -0.00010047 0.99999997 472.54212878
Axis -0.26838640 -0.54085960 -0.79714468
Axis point 18321.40668858 -515079.75430299 0.00000000
Rotation angle (degrees) 0.02145457
Shift along axis -662.36648984
> volume #1 level 0.001284
> hide #2 models
> show #2 models
> hide #!1 models
> show #!1 models
> volume #1 level 0.004186
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #2 models
> show #2 models
> hide #!1 models
> hide sel atoms
> show sel cartoons
> select /A4:751
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /BB:1061
6 atoms, 5 bonds, 1 residue, 1 model selected
> volume #1 level 0.006287
> volume #1 level 0.004786
> save /usr/local/model-
> angelo/hftv_turret_single_centred/Hftv1_turret_angelo_noSeq.cxs includeMaps
> true
[Errno 13] Permission denied: '/usr/local/model-
angelo/hftv_turret_single_centred/Hftv1_turret_angelo_noSeq.cxs.614198.tmp'
> save /home/alphafold/angelo_model/Hftv1_turret_angelo_NoSeq.cxs includeMaps
> true
> hide #!1 models
> hide #2 models
> open /home/alphafold/angelo_model/Hftv1_turret_angelo_NoSeq.cxs
Opened turret_small_box200_centred.mrc as #1, grid size 200,200,200, pixel
1.35, shown at level 0.00479, step 1, values float32
opened ChimeraX session
===== 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: 3.3.0 NVIDIA 510.85.02
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 125Gi 4.8Gi 21Gi 103Mi 99Gi 119Gi
Swap: 15Gi 734Mi 14Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2231] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:147e]
Kernel driver in use: nvidia
Locale: ('en_GB', 'UTF-8')
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-Clipper: 0.17.0
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-ISOLDE: 1.3
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-LinuxSupport: 1.0
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
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
distro: 1.6.0
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
line-profiler: 3.3.0
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
pexpect: 4.8.0
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
ptyprocess: 0.7.0
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
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
Change History (2)
comment:1 by , 3 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in event loop after session opened |
comment:2 by , 3 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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