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Opened 8 months ago
Closed 8 months ago
#17018 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.15.0-125-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00007fe0dd7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0ddffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0de7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/selectors.py", line 415 in select
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0deffd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0df7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0dffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0fcff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0fd7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0fdffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0fe7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0feffd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0ff7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe0fffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe11ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe13ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe15ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17cff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17d7fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17dffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17e7fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17effd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17f7fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe17ffff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a0ff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a17fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a1ffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a27fc700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a2ffd700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a37fe700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1a3fff700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1c4ff9700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1c57fa700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00007fe1c5ffb700 (most recent call first):
File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00007fe24e036740 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 464 in cxcmd
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 446 in defer
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 375 in thread_safe
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 455 in chimerax_intercept
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 353 in intercept
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 93 in _intercept
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/widgets/htmlview.py", line 320 in interceptRequest
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, PIL._imagingmath (total: 59)
===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/media/didier.poncet/Seagate Basic/papier CRYO/matos pour figures
> papier cryo/interactions tryp ring VP7.cxs"
opened ChimeraX session
> open "/home/didier.poncet/Documents/cryo wt:fox :RF/rec RF-Tryp.mrc" format
> mrc
Opened rec RF-Tryp.mrc as #2, grid size 600,600,600, pixel 1.76, shown at
level 0.0312, step 4, values float32
> volume #2 level 0.02188
> lighting soft
> volume #2 step 1
> transparency 50
> volume style mesh
> volume style surface
> volume #2 color #2e3436
> volume #2 color #888a85
> ui mousemode right "map eraser"
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> style sel sphere
Changed 39702 atom styles
> select subtract #1
Nothing selected
> select add #3
1 model selected
> ui mousemode right "translate selected models"
> view matrix models #3,1,0,0,750.29,0,1,0,523.11,0,0,1,700.04
> volume erase #2 center 750.29,523.11,700.04 radius 296.98
Opened rec RF-Tryp.mrc copy as #4, grid size 600,600,600, pixel 1.76, shown at
step 1, values float32
> view matrix models #3,1,0,0,736.73,0,1,0,533.04,0,0,1,685.54
> view matrix models #3,1,0,0,721.13,0,1,0,559.32,0,0,1,732.58
> view matrix models #3,1,0,0,698.38,0,1,0,750.05,0,0,1,663.41
> volume erase #4 center 698.38,750.05,663.41 radius 296.74
> view matrix models #3,1,0,0,728.44,0,1,0,573.46,0,0,1,350.13
> volume erase #4 center 728.44,573.46,350.13 radius 296.74
> view matrix models #3,1,0,0,548.48,0,1,0,257.99,0,0,1,382.86
> volume erase #4 center 548.48,257.99,382.86 radius 296.74
> view matrix models #3,1,0,0,579.59,0,1,0,468.43,0,0,1,760.62
> volume erase #4 center 579.59,468.43,760.62 radius 296.74
> view matrix models #3,1,0,0,644.93,0,1,0,356.8,0,0,1,639.26
> volume erase #4 center 644.93,356.8,639.26 radius 296.74
> view matrix models #3,1,0,0,630.97,0,1,0,381.24,0,0,1,651.77
> view matrix models #3,1,0,0,608.42,0,1,0,420.08,0,0,1,686.54
> view matrix models #3,1,0,0,296.7,0,1,0,369.62,0,0,1,780.99
> view matrix models #3,1,0,0,310.67,0,1,0,399.11,0,0,1,728.98
> volume erase #4 center 310.67,399.11,728.98 radius 296.74
> view matrix models #3,1,0,0,409.14,0,1,0,698.07,0,0,1,780.4
> volume erase #4 center 409.14,698.07,780.4 radius 296.74
> view matrix models #3,1,0,0,271.89,0,1,0,204.36,0,0,1,355.43
> volume erase #4 center 271.89,204.36,355.43 radius 296.74
> view matrix models #3,1,0,0,533.56,0,1,0,354.69,0,0,1,363.52
> view matrix models #3,1,0,0,463.05,0,1,0,512.97,0,0,1,130.73
> view matrix models #3,1,0,0,455.15,0,1,0,506.98,0,0,1,131.62
> volume erase #4 center 455.15,506.98,131.62 radius 101.9
> view matrix models #3,1,0,0,460.83,0,1,0,635.68,0,0,1,193.69
> volume erase #4 center 460.83,635.68,193.69 radius 101.9
> view matrix models #3,1,0,0,470.56,0,1,0,787.45,0,0,1,265.39
> volume erase #4 center 470.56,787.45,265.39 radius 101.9
> view matrix models #3,1,0,0,471.65,0,1,0,695.37,0,0,1,218.47
> view matrix models #3,1,0,0,505.24,0,1,0,871.37,0,0,1,290.7
> volume erase #4 center 505.24,871.37,290.7 radius 101.9
> view matrix models #3,1,0,0,540.02,0,1,0,840.73,0,0,1,415.85
> volume erase #4 center 540.02,840.73,415.85 radius 101.9
> view matrix models #3,1,0,0,480.96,0,1,0,806.1,0,0,1,484.7
> volume erase #4 center 480.96,806.1,484.7 radius 101.9
> view matrix models #3,1,0,0,588.49,0,1,0,824.51,0,0,1,545.21
> volume erase #4 center 588.49,824.51,545.21 radius 101.9
> view matrix models #3,1,0,0,620.05,0,1,0,936.23,0,0,1,398.34
> volume erase #4 center 620.05,936.23,398.34 radius 101.9
> view matrix models #3,1,0,0,622.86,0,1,0,855.45,0,0,1,336.91
> volume erase #4 center 622.86,855.45,336.91 radius 101.9
> view matrix models #3,1,0,0,762.53,0,1,0,864.12,0,0,1,358.08
> volume erase #4 center 762.53,864.12,358.08 radius 101.9
> view matrix models #3,1,0,0,505.71,0,1,0,91.967,0,0,1,337.98
> view matrix models #3,1,0,0,464.04,0,1,0,142.51,0,0,1,665.9
> volume erase #4 center 464.04,142.51,665.9 radius 101.9
> view matrix models #3,1,0,0,415.19,0,1,0,139.4,0,0,1,148.73
> view matrix models #3,1,0,0,667.81,0,1,0,394.08,0,0,1,260.95
> volume erase #4 center 667.81,394.08,260.95 radius 101.9
> view matrix models #3,1,0,0,681.67,0,1,0,478.08,0,0,1,198.88
> volume erase #4 center 681.67,478.08,198.88 radius 101.9
> view matrix models #3,1,0,0,646.51,0,1,0,394.28,0,0,1,83.054
> volume erase #4 center 646.51,394.28,83.054 radius 101.9
> view matrix models #3,1,0,0,489.72,0,1,0,429.05,0,0,1,51.399
> volume erase #4 center 489.72,429.05,51.399 radius 101.9
> view matrix models #3,1,0,0,602.49,0,1,0,606.73,0,0,1,173.69
> volume erase #4 center 602.49,606.73,173.69 radius 101.9
> view matrix models #3,1,0,0,589.54,0,1,0,559.84,0,0,1,209.23
> volume erase #4 center 589.54,559.84,209.23 radius 101.9
> view matrix models #3,1,0,0,464.26,0,1,0,512.23,0,0,1,522.39
> volume erase #4 center 464.26,512.23,522.39 radius 101.9
> view matrix models #3,1,0,0,314.5,0,1,0,747.02,0,0,1,680.36
> volume erase #4 center 314.5,747.02,680.36 radius 101.9
> view matrix models #3,1,0,0,329.99,0,1,0,724.15,0,0,1,666.6
> view matrix models #3,1,0,0,457.3,0,1,0,819.04,0,0,1,518.01
> volume erase #4 center 457.3,819.04,518.01 radius 101.9
> view matrix models #3,1,0,0,372.74,0,1,0,885.44,0,0,1,665.7
> volume erase #4 center 372.74,885.44,665.7 radius 101.9
> view matrix models #3,1,0,0,456.62,0,1,0,920.57,0,0,1,588.94
> volume erase #4 center 456.62,920.57,588.94 radius 101.9
> view matrix models #3,1,0,0,291.48,0,1,0,499.81,0,0,1,622.6
> volume erase #4 center 291.48,499.81,622.6 radius 101.9
> view matrix models #3,1,0,0,144.64,0,1,0,504.91,0,0,1,513.84
> volume erase #4 center 144.64,504.91,513.84 radius 101.9
> view matrix models #3,1,0,0,77.341,0,1,0,586.03,0,0,1,638.01
> volume erase #4 center 77.341,586.03,638.01 radius 101.9
> view matrix models #3,1,0,0,170.1,0,1,0,501.52,0,0,1,640.94
> volume erase #4 center 170.1,501.52,640.94 radius 101.9
> view matrix models #3,1,0,0,212.13,0,1,0,382.43,0,0,1,506.76
> volume erase #4 center 212.13,382.43,506.76 radius 101.9
> view matrix models #3,1,0,0,452.42,0,1,0,512.62,0,0,1,258.4
> volume erase #4 center 452.42,512.62,258.4 radius 101.9
> view matrix models #3,1,0,0,414.57,0,1,0,467.3,0,0,1,156.99
> volume erase #4 center 414.57,467.3,156.99 radius 101.9
> view matrix models #3,1,0,0,325.2,0,1,0,499.83,0,0,1,241.37
> volume erase #4 center 325.2,499.83,241.37 radius 101.9
> view matrix models #3,1,0,0,387.65,0,1,0,547.82,0,0,1,149.97
> volume erase #4 center 387.65,547.82,149.97 radius 101.9
> view matrix models #3,1,0,0,112.8,0,1,0,461.98,0,0,1,522.49
> volume erase #4 center 112.8,461.98,522.49 radius 101.9
> view matrix models #3,1,0,0,281.07,0,1,0,745.35,0,0,1,662.83
> volume erase #4 center 281.07,745.35,662.83 radius 101.9
> volume #2 level 0.02676
> undo
> hide #!2 models
Drag select of 4 rec RF-Tryp.mrc copy
> select subtract #4
Nothing selected
> volume #!4 style mesh
> select add #4
2 models selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 3 models selected
> fitmap #1 inMap #4
Fit molecule 18tryp.pdb (#1) to map rec RF-Tryp.mrc copy (#4) using 39702
atoms
average map value = 0.0263, steps = 60
shifted from previous position = 0.317
rotated from previous position = 0.287 degrees
atoms outside contour = 11854, contour level = 0.021881
Position of 18tryp.pdb (#1) relative to rec RF-Tryp.mrc copy (#4) coordinates:
Matrix rotation and translation
0.99999436 -0.00032785 0.00334127 -1.10511183
0.00034029 0.99999301 -0.00372238 1.49731264
-0.00334002 0.00372350 0.99998749 -1.89094093
Axis 0.74263322 0.66637465 0.06663881
Axis point 0.00000000 510.07102039 392.14607596
Rotation angle (degrees) 0.28723440
Shift along axis 0.05106838
> view matrix models
> #1,0.99999,-0.00032785,0.0033413,66.475,0.00034029,0.99999,-0.0037224,68.43,-0.00334,0.0037235,0.99999,-103.69,#4,1,0,0,67.58,0,1,0,66.932,0,0,1,-101.8
> select subtract #4
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #3
1 model selected
> view matrix models #3,1,0,0,446.89,0,1,0,493.18,0,0,1,358.75
> view matrix models #3,1,0,0,697.28,0,1,0,846.19,0,0,1,268.37
> volume erase #4 center 697.28,846.19,268.37 radius 101.9
> view matrix models #3,1,0,0,589.96,0,1,0,722.33,0,0,1,-85.034
> volume erase #4 center 589.96,722.33,-85.034 radius 101.9
> view matrix models #3,1,0,0,321.06,0,1,0,788.02,0,0,1,239.6
> view matrix models #3,1,0,0,326.71,0,1,0,768.55,0,0,1,292.92
> view matrix models #3,1,0,0,324.49,0,1,0,761.83,0,0,1,304.52
> volume erase #4 center 324.49,761.83,304.52 radius 235.49 outside true
> select subtract #3
Nothing selected
> select add #4
2 models selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 3 models selected
> view matrix models
> #1,0.99999,-0.00032785,0.0033413,30.063,0.00034029,0.99999,-0.0037224,-80.698,-0.00334,0.0037235,0.99999,-265.9,#4,1,0,0,31.169,0,1,0,-82.195,0,0,1,-264.01
> transparency sel 50
> volume sel style image
> volume sel style surface
> volume sel style mesh
> select add #4
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select add #4
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> show sel cartoons
> hide sel atoms
> view matrix models
> #1,0.99999,-0.00032785,0.0033413,106.91,0.00034029,0.99999,-0.0037224,-51.735,-0.00334,0.0037235,0.99999,-352.04,#4,1,0,0,108.01,0,1,0,-53.232,0,0,1,-350.15
> volume #2 level 0.0193
> hide #!2 models
> select add #4
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select add #4
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> volume #4 change image level -2.132e-06,0 level 0.004789,0.8 level 0.05064,1
> volume #4 step 2
> volume #4 level 0.01613
> select add #4
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select subtract #1
3 models selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select subtract #1
3 models selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select add #4
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select subtract #1
3 models selected
> select add #4
3 models selected
> hide #!4 models
> show #!4 models
> hide #1 models
> show #1 models
> transparency sel 0
> volume sel style mesh
> select add #4
3 models selected
> select add #4
3 models selected
> show #!4 target m
> transparency sel 50
> transparency sel 0
> volume sel style surface
> select add #4
3 models selected
> hide #!4 models
> show #!4 models
> transparency sel 50
> lighting soft
> select add #4
3 models selected
> lighting full
> set bgColor black
> set bgColor gray
> set bgColor white
> color #4 #b2b2b280 models
> color #4 #eeeeecff models
> color #4 #f3f3f3ff models
> color #4 white models
> color #4 #d3d7cfff models
> color #4 #a440bfff models
> color #4 #7040bfff models
> color #4 #bf4d40ff models
> color #4 #40bf74ff models
> color #4 #40bf74ec models
> color #4 #40bf744b models
> color #4 #40bf7435 models
> color #4 #bfb74035 models
> color #4 #bfbe4035 models
> color #4 #b1bf4035 models
> color #4 #adbf4035 models
> ui tool show "Side View"
> graphics silhouettes true
> graphics silhouettes false
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> rainbow sel
> show sel cartoons
> undo
> hide sel cartoons
> show sel cartoons
> view #4 clip false
> color sel bychain
> color #1 #ef2929ff
> open "/media/didier.poncet/Seagate Basic/papier CRYO/matos pour figures
> papier cryo/Trypsin ring VP7/18 tryp ring VP7 couleur.cxs"
opened ChimeraX session
> open "/home/didier.poncet/Documents/cryo wt:fox :RF/rec RF-Tryp.mrc" format
> mrc
Opened rec RF-Tryp.mrc as #2, grid size 600,600,600, pixel 1.76, shown at
level 0.0312, step 4, values float32
> volume #2 level 0.01792
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> style sel sphere
Changed 39702 atom styles
> show sel cartoons
> hide #!2 models
> select subtract #1
Nothing selected
> show #!2 models
> volume style image
> volume style surface
> transparency 50
> lighting soft
> lighting full
> lighting soft
> lighting simple
> lighting soft
> color #2 #babdb6ff models
> color #2 #d3d7cfff models
> transparency 50
> set bgColor gray
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T
1629 atoms, 1660 bonds, 223 residues, 1 model selected
> color sel lime
> show sel cartoons
> hide sel surfaces
> show sel cartoons
> hide sel atoms
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:16-17
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui mousemode right "translate selected models"
> select add #2
8 atoms, 7 bonds, 1 residue, 4 models selected
> view matrix models
> #1,1,0,0,85.545,0,1,0,183.56,0,0,1,-18.645,#2,1,0,0,85.545,0,1,0,183.56,0,0,1,-18.645
> volume #2 step 1
> volume #2 change image level -0.003643,0 level 0.03117,0.8 level 0.04921,1
> volume #2 level 0.02253
> transparency sel 0
> transparency sel 50
> save "/home/didier.poncet/Documents/superpo ring VP7 map tryp.cxs"
> includeMaps true
> lighting soft
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> select subtract #1
3 models selected
> color #2 #f57900ff models
> transparency sel 50
> color #2 #fce94fff models
> transparency sel 50
> color #2 #d3d7cfff models
> transparency sel 50
> color #2 #2e3436ff models
> color #2 #d3d7cfff models
> transparency sel 50
> set bgColor white
> set bgColor gray
> volume #2 level 0.02505
> volume #2 level 0.02673
> volume #2 level 0.01121
> select add #2
3 models selected
> select add #2
3 models selected
> view sel
> select /T:16-48
223 atoms, 228 bonds, 31 residues, 1 model selected
> select /T
1629 atoms, 1660 bonds, 223 residues, 1 model selected
> view sel
> view matrix models #1,1,0,0,88.247,0,1,0,181.33,0,0,1,-24.508
> undo
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T
1629 atoms, 1660 bonds, 223 residues, 1 model selected
> select /T:18
4 atoms, 3 bonds, 1 residue, 1 model selected
> select /T:18
4 atoms, 3 bonds, 1 residue, 1 model selected
> color #2 #babdb6ff models
> transparency 50
> set bgColor white
> color #2 #888a85ff models
> transparency 50
> save "/home/didier.poncet/Documents/ring VP7 tryp RF tryp view.png" width
> 1525 height 1200 supersample 3 transparentBackground true
> select /T:56-58,165-171,231-233,235-243
161 atoms, 160 bonds, 22 residues, 1 model selected
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel cartoons
> show sel atoms
> style sel stick
Changed 10 atom styles
> color sel yellow
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 8 atom styles
> color sel magenta
> select /T:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /T:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> style sel stick
Changed 6 atom styles
> color sel magenta
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T
1629 atoms, 1660 bonds, 223 residues, 1 model selected
> view sel
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/home/didier.poncet/Documents/tryp dans canal side view.png" width
> 1525 height 1200 supersample 3 transparentBackground true
> volume #2 level 0.01302
> volume #2 level 0.01
> volume #2 level 0.015
> lighting full
> save "/home/didier.poncet/Documents/ring VP7 tryp TLP tryp side view.png"
> width 1525 height 1200 supersample 3 transparentBackground true
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /T:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /T:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> view sel
> undo
> color sel orange red
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /T:57
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel orange red
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:102,H:57
18 atoms, 17 bonds, 2 residues, 1 model selected
> select /T:102,H:57,S:195
24 atoms, 22 bonds, 3 residues, 1 model selected
> color sel red
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:102
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /T:195
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> select /T:102,T:195,T:57
24 atoms, 22 bonds, 3 residues, 1 model selected
> style sel sphere
Changed 24 atom styles
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> save "/home/didier.poncet/Documents/tryp activ site side view.png" width
> 1525 height 1200 supersample 3 transparentBackground true
> ui mousemode right "rotate selected models"
> ui mousemode right "translate selected models"
> volume #2 step 2
> ui mousemode right "rotate selected models"
> volume #2 level 0.01444
> volume #2 step 1
> volume #2 level 0.014
> transparency 0
> transparency 50
> lighting full
> lighting simple
> lighting soft
> lighting full
> volume style mesh
> save "/home/didier.poncet/Documents/tryspine side view mesh.png" width 1525
> height 1200 supersample 3 transparentBackground true
> select /T:102,T:195,T:57
24 atoms, 22 bonds, 3 residues, 1 model selected
> style sel stick
Changed 24 atom styles
> style sel ball
Changed 24 atom styles
> color sel magenta
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> view matrix models
> #1,0.96084,0.269,0.066542,-118.12,-0.24311,0.93352,-0.2635,393.03,-0.133,0.237,0.96236,-136.07
> undo
> select add #2
39702 atoms, 40531 bonds, 5038 residues, 4 models selected
> view matrix models
> #1,0.99918,0.038053,0.014023,58.484,-0.037509,0.9986,-0.037203,223.74,-0.015419,0.036646,0.99921,-29.436,#2,0.99918,0.038053,0.014023,58.484,-0.037509,0.9986,-0.037203,223.74,-0.015419,0.036646,0.99921,-29.436
> ui mousemode right pivot
> ui mousemode right "rotate selected models"
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> view matrix models
> #1,0.99918,0.038053,0.014023,27.89,-0.037509,0.9986,-0.037203,196.97,-0.015419,0.036646,0.99921,-49.288,#2,0.99918,0.038053,0.014023,27.89,-0.037509,0.9986,-0.037203,196.97,-0.015419,0.036646,0.99921,-49.288
> select subtract #1
3 models selected
> select add #2
3 models selected
> select /T:16-48
223 atoms, 228 bonds, 31 residues, 1 model selected
> select /T:16-183,184,184A,185-187,188,188A,189-220,221,221A,222-244
1620 atoms, 1651 bonds, 222 residues, 1 model selected
> view sel
> transparency 0
> transparency 50
> volume style surface
> transparency 0
> transparency 50
> select /T:102,T:195,T:57
24 atoms, 22 bonds, 3 residues, 1 model selected
> view sel
> view
> view sel
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> select add #2
5 models selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 6 models selected
> volume sel style surface
> view
> lighting soft
> lighting full
> volume #2 level 0.01568
> lighting full
> lighting soft
> lighting full
> lighting simple
> lighting full
> volume #2 level 0.015
> view sel
> select subtract #1
3 models selected
> select add #2
3 models selected
> select /T:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /T
1629 atoms, 1660 bonds, 223 residues, 1 model selected
> view sel
> view matrix models
> #1,0.99918,0.038053,0.014023,28.402,-0.037509,0.9986,-0.037203,181.97,-0.015419,0.036646,0.99921,-36.605
> undo
> redo
> undo
> fitmap #1 inMap #2
Fit molecule 18tryp.pdb (#1) to map rec RF-Tryp.mrc (#2) using 39702 atoms
average map value = 0.0263, steps = 60
shifted from previous position = 0.317
rotated from previous position = 0.287 degrees
atoms outside contour = 4000, contour level = 0.015
Position of 18tryp.pdb (#1) relative to rec RF-Tryp.mrc (#2) coordinates:
Matrix rotation and translation
0.99999436 -0.00032781 0.00334125 -1.10515525
0.00034024 0.99999301 -0.00372238 1.49727360
-0.00334001 0.00372350 0.99998749 -1.89094514
Axis 0.74263489 0.66637371 0.06662958
Axis point 0.00000000 510.07133582 392.14361753
Rotation angle (degrees) 0.28723369
Shift along axis 0.05102402
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select add #2
39702 atoms, 40531 bonds, 5038 residues, 6 models selected
> view matrix models
> #1,0.99914,0.037777,0.01722,28.143,-0.037044,0.99847,-0.041045,180.62,-0.018744,0.040372,0.99901,-34.075,#2,0.99918,0.038053,0.014023,29.217,-0.037509,0.9986,-0.037203,179.01,-0.015419,0.036646,0.99921,-32.257
> ui mousemode right "rotate selected models"
> select subtract #1
5 models selected
> select add #2
5 models selected
> select add #2
5 models selected
> hide #!2 models
> show #!2 models
> select add #2.1
5 models selected
> select add #2.2
5 models selected
> select add #2.2
5 models selected
> select add #2.2
5 models selected
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 6 models selected
> select subtract #2.1
39702 atoms, 40531 bonds, 5038 residues, 3 models selected
> select subtract #1
2 models selected
> save "/home/didier.poncet/Documents/vu canal top.png" width 1525 height 1200
> supersample 3 transparentBackground true
> select /T:102,T:195,T:57
24 atoms, 22 bonds, 3 residues, 1 model selected
> color sel magenta
> select add #1
39702 atoms, 40531 bonds, 5038 residues, 1 model selected
> select subtract #1
Nothing selected
> save /home/didier.poncet/image1.png supersample 3
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie5.mp4
Movie saved to /home/didier.poncet/movie5.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie6.mp4
Movie saved to /home/didier.poncet/movie6.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie7.mp4
Movie saved to /home/didier.poncet/movie7.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie8.mp4
Movie saved to /home/didier.poncet/movie8.mp4
> transparency 0
> transparency 50
> save "/home/didier.poncet/Documents/active site from inside.png" width 1525
> height 1200 supersample 3 transparentBackground true
> save "/home/didier.poncet/Documents/active site from inside x4.png" width
> 1525 height 1200 supersample 4 transparentBackground true
> open "/home/didier.poncet/Documents/superpo tryp densite diff apro.cxs"
> format session
Opened rec RF-fox.mrc as #2, grid size 600,600,600, pixel 1.76, shown at level
0.0222, step 2, values float32
Opened rec RF-Tryp.mrc as #3, grid size 600,600,600, pixel 1.76, shown at
level 0.0218, step 1, values float32
Opened run_class001-rfapro3A-mirrorX-176pix-600box.mrc as #1, grid size
600,600,600, pixel 1.69, shown at level 0.0145, step 1, values float32
Opened rec SA VP7 RF Q201-Tryp.mrc as #7, grid size 600,600,600, pixel 1.76,
shown at level 0.015, step 1, values float32
Opened rec SA VP7 RF-Tryp.mrc as #8, grid size 600,600,600, pixel 1.76, shown
at level 0.025, step 1, values float32
Opened volume difference as #5, grid size 600,600,600, pixel 1.76, shown at
level 0.03, step 2, values float32
Opened volume difference copy as #10, grid size 600,600,544, pixel 1.76, shown
at level 0.0159, step 1, values float32
opened ChimeraX session
> show sel cartoons
> open "/home/didier.poncet/Documents/superpo tryp densite diff apro.cxs"
> format session
Opened rec RF-fox.mrc as #2, grid size 600,600,600, pixel 1.76, shown at level
0.0222, step 2, values float32
Opened rec RF-Tryp.mrc as #3, grid size 600,600,600, pixel 1.76, shown at
level 0.0218, step 1, values float32
Opened run_class001-rfapro3A-mirrorX-176pix-600box.mrc as #1, grid size
600,600,600, pixel 1.69, shown at level 0.0145, step 1, values float32
Opened rec SA VP7 RF Q201-Tryp.mrc as #7, grid size 600,600,600, pixel 1.76,
shown at level 0.015, step 1, values float32
Opened rec SA VP7 RF-Tryp.mrc as #8, grid size 600,600,600, pixel 1.76, shown
at level 0.025, step 1, values float32
Opened volume difference as #5, grid size 600,600,600, pixel 1.76, shown at
level 0.03, step 2, values float32
Opened volume difference copy as #10, grid size 600,600,544, pixel 1.76, shown
at level 0.0159, step 1, values float32
opened ChimeraX session
> view matrix models
> #6,-0.12382,0.91977,-0.37241,335.72,-0.24467,-0.39201,-0.88683,784.64,-0.96167,-0.018687,0.27358,743.47
> set bgColor white
> transparency #10.1 50
> volume #!10 style surface
> transparency #10.1 0
> volume #!10 style surface
> transparency #10.1 50
> select add #4
58122 atoms, 59012 bonds, 10 pseudobonds, 7261 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> select subtract #4
4135 atoms, 3882 bonds, 10 pseudobonds, 514 residues, 2 models selected
> hide #!6 models
> show #!6 models
> view sel
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select subtract #6.1
4135 atoms, 3882 bonds, 514 residues, 1 model selected
> hide #6.1 models
> select add #6
4135 atoms, 3882 bonds, 10 pseudobonds, 514 residues, 2 models selected
> select subtract #6.1
4135 atoms, 3882 bonds, 514 residues, 1 model selected
> select #6/A:26-58
439 atoms, 446 bonds, 31 residues, 1 model selected
> select #6/A:26-102
1118 atoms, 1131 bonds, 74 residues, 1 model selected
> select
> #6/A:20-21,30-34,40-48,51-54,64-67,81-90,104-108,135-140,156-161,180-183,198-201,204-215,226-230
1141 atoms, 1140 bonds, 72 residues, 1 model selected
> select #6/A:26-102
1118 atoms, 1131 bonds, 74 residues, 1 model selected
> select /T:102,T:195,T:57
Nothing selected
> select /A:102,A:195,A:57
58 atoms, 54 bonds, 5 residues, 2 models selected
> color (#!6 & sel) magenta
> show sel & #!6 atoms
> style sel & #!6 stick
Changed 41 atom styles
> select add #6
4152 atoms, 3897 bonds, 10 pseudobonds, 516 residues, 3 models selected
> select add #10
4152 atoms, 3897 bonds, 10 pseudobonds, 516 residues, 6 models selected
> fitmap #6 inMap #10
Fit molecule 1s81 (#6) to map volume difference copy (#10) using 4135 atoms
average map value = 0.01095, steps = 104
shifted from previous position = 0.637
rotated from previous position = 34.5 degrees
atoms outside contour = 3083, contour level = 0.015888
Position of 1s81 (#6) relative to volume difference copy (#10) coordinates:
Matrix rotation and translation
-0.34599089 0.89855808 0.26996985 346.59449257
-0.60601601 0.00563878 -0.79543248 787.95369266
-0.71626457 -0.43881844 0.54258960 776.76844126
Axis 0.19444549 0.53774898 -0.82037613
Axis point 611.55602140 498.73298751 0.00000000
Rotation angle (degrees) 113.50825852
Shift along axis -146.12725694
> volume #10 level 0.01496
> select subtract #6
17 atoms, 15 bonds, 2 residues, 4 models selected
> select subtract #10
17 atoms, 15 bonds, 2 residues, 1 model selected
> select #6/A:16
21 atoms, 20 bonds, 1 residue, 1 model selected
> select #6/A:16-183,184,184A,185-187,188,188A,189-220,221,221A,222-245
3243 atoms, 3281 bonds, 223 residues, 1 model selected
> color sel forest green
> color sel light sea green
> color sel lime
> color sel orange
> color sel forest green
> select /A:102,A:195,A:57
58 atoms, 54 bonds, 5 residues, 2 models selected
> color (#!6 & sel) lime
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie9.mp4
Movie saved to /home/didier.poncet/movie9.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie10.mp4
Movie saved to /home/didier.poncet/movie10.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie11.mp4
Movie saved to /home/didier.poncet/movie11.mp4
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie12.mp4
Movie saved to /home/didier.poncet/movie12.mp4
> color #10 #b2b2b280 models
> color #10 #888a8580 models
> color #10 #b2b2b280 models
> lighting soft
> lighting full
> select /A:102,A:195,A:57
58 atoms, 54 bonds, 5 residues, 2 models selected
> hide sel & #!6 atoms
> show sel & #!6 atoms
> style sel & #!6 ball
Changed 41 atom styles
> nucleotides sel & #!6 atoms
> style nucleic & sel & #!6 stick
Changed 0 atom styles
> style sel & #!6 stick
Changed 41 atom styles
> color #10 #adbf4035 models
> color #10 #888a8580 models
> color #10 #adbf4035 models
> color #10 #888a8580 models
> set bgColor gray
> set bgColor white
> lighting soft
> lighting full
> lighting simple
> movie record
> turn y 2 180
> wait 180
> movie encode /home/didier.poncet/movie13.mp4
Movie saved to /home/didier.poncet/movie13.mp4
> ui tool show "Selection Inspector"
> help help:user/tools/inspector.html
> open "/home/didier.poncet/Documents/superpo ring VP7 map tryp.cxs" format
> session
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "/home/didier.poncet/Documents/cryo wt:mut:SA11/rec SA VP7 RF
> Q201-Tryp.mrc"
Opened rec SA VP7 RF Q201-Tryp.mrc as #1, grid size 600,600,600, pixel 1.76,
shown at level 0.0286, step 4, values float32
OpenGL version: 3.3.0 NVIDIA 535.183.06
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: fr_FR.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:3
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 48 AMD Ryzen Threadripper 3960X 24-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 188Gi 9.0Gi 30Gi 83Mi 149Gi 177Gi
Swap: 2.0Gi 451Mi 1.6Gi
Graphics:
01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:24b0] (rev a1)
Subsystem: NVIDIA Corporation Device [10de:14ad]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2023.11.17
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 23.2
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 8 months ago
| Component: | Unassigned → Core |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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