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Opened 15 months ago
Closed 15 months ago
#15675 closed defect (duplicate)
Crash in garbage collection
| 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-5.15.0-113-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Aborted
Thread 0x00007fc7377fe700 (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 0x00007fc737fff700 (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 0x00007fc754ff9700 (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 0x00007fc7557fa700 (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 0x00007fc755ffb700 (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 0x00007fc7567fc700 (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 0x00007fc756ffd700 (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 0x00007fc7577fe700 (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 0x00007fc757fff700 (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 0x00007fc774ff9700 (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 0x00007fc7757fa700 (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 0x00007fc775ffb700 (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 0x00007fc7767fc700 (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 0x00007fc776ffd700 (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 0x00007fc7777fe700 (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 0x00007fc777fff700 (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 0x00007fc794ff9700 (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 0x00007fc7957fa700 (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 0x00007fc795ffb700 (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 0x00007fc7967fc700 (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 0x00007fc796ffd700 (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 0x00007fc7977fe700 (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 0x00007fc797fff700 (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 0x00007fc7b4ff9700 (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 0x00007fc7b57fa700 (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 0x00007fc7b5ffb700 (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 0x00007fc7b67fc700 (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 0x00007fc7b6ffd700 (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 0x00007fc7b77fe700 (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 0x00007fc7b7fff700 (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 0x00007fc7d4ff9700 (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 0x00007fc7d57fa700 (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 0x00007fc7d5ffb700 (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 0x00007fc7d67fc700 (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 0x00007fc7d6ffd700 (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 0x00007fc7d77fe700 (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 0x00007fc7d7fff700 (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 0x00007fc7f4ff9700 (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 0x00007fc7f57fa700 (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 0x00007fc7f5ffb700 (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 0x00007fc7f67fc700 (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 0x00007fc7f6ffd700 (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 0x00007fc7f77fe700 (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 0x00007fc7f7fff700 (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 0x00007fc814ff9700 (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 0x00007fc8157fa700 (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 0x00007fc815ffb700 (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 0x00007fc8167fc700 (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 0x00007fc816ffd700 (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 0x00007fc8177fe700 (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 0x00007fc817fff700 (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 0x00007fc8dff88740 (most recent call first):
Garbage-collecting
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/numpy/core/_internal.py", line 255 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 251 in set_cvec_pointer
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 133 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 894 in __init__
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2226 in process_changes
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 2231 in changes
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/changes.py", line 36 in check_for_changes
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 69 in draw_new_frame
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
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, openmm._openmm, openmm.app.internal.compiled, 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, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.linalg._flinalg, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.optimize._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 123)
===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /home/alphafold/Cryo-
> Em/Ribosome/Ecoli/cryo/eBIC/maps/cryosparc_P28_J881_008_volume_map.mrc
Opened cryosparc_P28_J881_008_volume_map.mrc as #1, grid size 480,480,480,
pixel 0.645, shown at level 0.0699, step 2, values float32
> open /home/alphafold/Cryo-
> Em/Ribosome/coxiella/cryo/modelling/final_models/23_16S_v1.pdb
Chain information for 23_16S_v1.pdb
---
Chain | Description
2.1/23 | No description available
2.2/a | No description available
> select clear
> volume #1 level 0.03979
> select add #2
94445 atoms, 105629 bonds, 4510 residues, 3 models selected
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.21317,0.95936,-0.18491,-40.628,0.19065,0.14477,0.97092,-96.391,0.95823,-0.24223,-0.15204,36.86
> view matrix models
> #2,0.22287,0.78817,-0.57369,71.572,0.050787,0.5783,0.81424,-122.75,0.97352,-0.21061,0.088858,-21.367
> view matrix models
> #2,0.22287,0.78817,-0.57369,62.768,0.050787,0.5783,0.81424,-128.53,0.97352,-0.21061,0.088858,-12.991
> view matrix models
> #2,0.22287,0.78817,-0.57369,62.664,0.050787,0.5783,0.81424,-127.57,0.97352,-0.21061,0.088858,-14.594
> view matrix models
> #2,0.22287,0.78817,-0.57369,62.61,0.050787,0.5783,0.81424,-131.4,0.97352,-0.21061,0.088858,-9.6659
> view matrix models
> #2,0.24072,0.77515,-0.58412,63.735,0.099223,0.57901,0.80926,-140.11,0.96551,-0.25276,0.062465,5.4922
> fitmap #2 inMap #1
Fit molecules 23_16S_v1.pdb (#2.1), 23_16S_v1.pdb (#2.2) to map
cryosparc_P28_J881_008_volume_map.mrc (#1) using 94445 atoms
average map value = 0.08094, steps = 148
shifted from previous position = 8.2
rotated from previous position = 4.09 degrees
atoms outside contour = 18134, contour level = 0.039793
Position of 23_16S_v1.pdb (#2.1) relative to
cryosparc_P28_J881_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99944525 -0.00788301 -0.03235803 6.98627370
0.00990649 0.99797331 0.06285807 -8.55257180
0.03179694 -0.06314376 0.99749778 1.40357210
Axis -0.88416812 -0.45018220 0.12483076
Axis point 0.00000000 20.45325570 152.13071454
Rotation angle (degrees) 4.08604192
Shift along axis -2.15161598
Position of 23_16S_v1.pdb (#2.2) relative to
cryosparc_P28_J881_008_volume_map.mrc (#1) coordinates:
Matrix rotation and translation
0.99944525 -0.00788301 -0.03235803 6.98627370
0.00990649 0.99797331 0.06285807 -8.55257180
0.03179694 -0.06314376 0.99749778 1.40357210
Axis -0.88416812 -0.45018220 0.12483076
Axis point 0.00000000 20.45325570 152.13071454
Rotation angle (degrees) 4.08604192
Shift along axis -2.15161598
> select #2/23:2589@N1
1 atom, 1 residue, 1 model selected
> view sel
> select #2/23:2066@N1
Nothing selected
> ui tool show "Side View"
> select #2/23:4029@N1
1 atom, 1 residue, 1 model selected
> view sel
> open /home/alphafold/Cryo-
> Em/Ribosome/coxiella/cryo/modelling/50S_DXT/50S_DXT-coot-3.cif
Summary of feedback from opening /home/alphafold/Cryo-
Em/Ribosome/coxiella/cryo/modelling/50S_DXT/50S_DXT-coot-3.cif
---
warnings | Unable to fetch template for '---': will connect using distance
criteria
Atom H213 is not in the residue template for DXT /DXT:1
Atom H213 is not in the residue template for DXT /DXT:2
Atom H213 is not in the residue template for DXT /DXT:3
Atom . is not in the residue template for DXT /DXT:4
Atom . is not in the residue template for DXT /DXT:5
> ui mousemode right "translate selected models"
> view matrix models
> #2.1,0.99945,-0.007883,-0.032358,-23.316,0.0099065,0.99797,0.062858,-15.836,0.031797,-0.063144,0.9975,8.6076
> undo
> select clear
> select add #3
288 atoms, 301 bonds, 8 residues, 1 model selected
> view matrix models #3,1,0,0,-44.778,0,1,0,-58.656,0,0,1,-30.682
> select #2/23:4029@N1
1 atom, 1 residue, 1 model selected
> view sel
> select clear
> select add #3
288 atoms, 301 bonds, 8 residues, 1 model selected
> view matrix models #3,1,0,0,-46.402,0,1,0,-53.615,0,0,1,-33.341
> view matrix models
> #3,0.99113,-0.093619,-0.09429,-0.53494,0.079446,0.98635,-0.14423,-35.632,0.10651,0.13546,0.98504,-86.604
> view matrix models
> #3,0.97865,0.066311,-0.19457,-11.346,0.011236,0.92787,0.37274,-126.49,0.20525,-0.36697,0.90731,24.893
> view matrix models
> #3,0.85228,0.12613,-0.50765,77.786,0.13829,0.88163,0.45122,-164.2,0.50447,-0.45477,0.73396,14.766
> view matrix models
> #3,0.85228,0.12613,-0.50765,71.146,0.13829,0.88163,0.45122,-153.53,0.50447,-0.45477,0.73396,15.386
> view matrix models
> #3,0.85228,0.12613,-0.50765,70.146,0.13829,0.88163,0.45122,-154.28,0.50447,-0.45477,0.73396,15.689
> view matrix models
> #3,0.68516,0.30813,-0.66001,103.05,-0.045857,0.92257,0.38311,-104.21,0.72695,-0.23222,0.64623,-68.35
> view matrix models
> #3,0.68516,0.30813,-0.66001,95.985,-0.045857,0.92257,0.38311,-111.41,0.72695,-0.23222,0.64623,-60.644
> view matrix models
> #3,0.68516,0.30813,-0.66001,94.389,-0.045857,0.92257,0.38311,-111.68,0.72695,-0.23222,0.64623,-59.101
> view matrix models
> #3,0.7406,-0.16992,-0.65011,190.04,0.062762,0.98076,-0.18484,-18.447,0.66901,0.096089,0.73702,-142.85
> view matrix models
> #3,0.7406,-0.16992,-0.65011,185.38,0.062762,0.98076,-0.18484,-19.537,0.66901,0.096089,0.73702,-139.38
> view matrix models
> #3,0.7406,-0.16992,-0.65011,184.22,0.062762,0.98076,-0.18484,-22.168,0.66901,0.096089,0.73702,-137.44
> view matrix models
> #3,0.7406,-0.16992,-0.65011,184.19,0.062762,0.98076,-0.18484,-22.48,0.66901,0.096089,0.73702,-137.22
> view matrix models
> #3,0.7406,-0.16992,-0.65011,181.97,0.062762,0.98076,-0.18484,-22.44,0.66901,0.096089,0.73702,-135.12
> view matrix models
> #3,0.704,-0.086172,-0.70496,183.99,0.052889,0.99622,-0.068958,-50.731,0.70823,0.011262,0.70589,-117.45
> view matrix models
> #3,0.704,-0.086172,-0.70496,181.97,0.052889,0.99622,-0.068958,-47.612,0.70823,0.011262,0.70589,-115.46
> view matrix models
> #3,0.704,-0.086172,-0.70496,181.05,0.052889,0.99622,-0.068958,-47.372,0.70823,0.011262,0.70589,-117.17
> hide #!2 models
> show #!1 models
> view matrix models
> #3,0.704,-0.086172,-0.70496,181.18,0.052889,0.99622,-0.068958,-47.486,0.70823,0.011262,0.70589,-117.04
> volume #1 level 0.03195
> view matrix models
> #3,0.704,-0.086172,-0.70496,181.96,0.052889,0.99622,-0.068958,-46.459,0.70823,0.011262,0.70589,-117.08
> view matrix models
> #3,0.704,-0.086172,-0.70496,181.48,0.052889,0.99622,-0.068958,-46.782,0.70823,0.011262,0.70589,-116.43
Drag select of 98 atoms, 98 bonds
Drag select of 174 atoms, 180 bonds
> molmap sel 15
Opened 50S_DXT-coot-3.cif map 15 as #4, grid size 21,22,21, pixel 5, shown at
level 0.0101, step 1, values float32
> select #4
2 models selected
> hide #!4 models
> hide #3 models
> show #3 models
> show #!4 models
> hide #3 models
> vop resample #4 ongrid #1
Opened 50S_DXT-coot-3.cif map 15 resampled as #5, grid size 480,480,480, pixel
0.645, shown at step 1, values float32
> vop resample #4 ongrid #1
Opened 50S_DXT-coot-3.cif map 15 resampled as #6, grid size 480,480,480, pixel
0.645, shown at step 1, values float32
> close #5
> save /home/alphafold/Cryo-
> Em/Ribosome/Ecoli/cryo/eBIC/masks/dxt_50S_forclassification.mrc models #6
> save /alphafold-
> libs/otter/shared/will/ecoli_dxt_classification/dxt_50S_ecoli_forClassification.mrc
> models #6
> close
> open /home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz
Summary of feedback from opening
/home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz
---
warnings | WARNING: multiple experimental reflection datasets found:
(dataset) HKL_base,
(dataset) F, SIGF
Automatically choosing "(dataset) F, SIGF".
No free flags detected in this dataset! Automatically generated a new random
set with 2085 free from 177649 observed reflections. You should save your data
to a new MTZ file and use this for any future rebuilding/refinement.
notes |
| Chain information for 0017-01_refmacat.pdb #1
---
Chain
| Description
A
| No description available
B I
| No description available
C
| No description available
D
| No description available
E J
| No description available
F L
| No description available
G
| No description available
H K
| No description available
Discarding unrecognised/unsupported data array /xw941/SAD/FOM W
Launching live xmap mgr took 2.780285596847534 seconds.
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.62, step 1, values float32
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level -0.188,0.188, step 1, values float32
Opened (LIVE) 2mFo-DFc_smooth_8 as #1.1.1.4, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.219, step 1, values float32
Opened (STATIC) (dataset) FC, PHIC as #1.1.1.5, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.559, step 1, values float32
Opened (STATIC) (dataset) FC_ALL, PHIC_ALL as #1.1.1.6, grid size 46,44,42,
pixel 0.579,0.578,0.581, shown at level -0.481,0.481, step 1, values float32
Opened (STATIC) (dataset) FWT, PHWT as #1.1.1.7, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.433, step 1, values float32
Opened (STATIC) (dataset) DELFWT, PHDELWT as #1.1.1.8, grid size 46,44,42,
pixel 0.579,0.578,0.581, shown at level -0.201,0.201, step 1, values float32
Opened (STATIC) (dataset) FAN, PHAN as #1.1.1.9, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level -0.0361,0.0361, step 1, values float32
Opened (STATIC) (dataset) DELFAN, PHDELAN as #1.1.1.10, grid size 46,44,42,
pixel 0.579,0.578,0.581, shown at level -0.0361,0.0361, step 1, values float32
Opened (STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS as #1.1.1.11, grid size
46,44,42, pixel 0.579,0.578,0.581, shown at level -0.501,0.501, step 1, values
float32
Chain information for 0017-01_refmacat.pdb
---
Chain | Description
1.2/A | No description available
1.2/B 1.2/I | No description available
1.2/C | No description available
1.2/D | No description available
1.2/E 1.2/J | No description available
1.2/F 1.2/L | No description available
1.2/G | No description available
1.2/H 1.2/K | No description available
Opened crystallographic dataset from
/home/alphafold/Downloads/OneDrive_1_24-07-2024/0017-01_refmacat.mtz
Found experimental reflection data:
(dataset) F, SIGF
Rwork: 0.2682; Rfree: 0.2681
Generated maps:
Reflection Data
(LIVE) 2mFo-DFc
(LIVE) mFo-DFc
(LIVE) 2mFo-DFc_smooth_8
(STATIC) (dataset) FC, PHIC
(STATIC) (dataset) FC_ALL, PHIC_ALL
(STATIC) (dataset) FWT, PHWT
(STATIC) (dataset) DELFWT, PHDELWT
(STATIC) (dataset) FAN, PHAN
(STATIC) (dataset) DELFAN, PHDELAN
(STATIC) (dataset) FC_ALL_LS, PHIC_ALL_LS
Any unwanted maps may be safely closed via the Model panel.
> isolde start
> set selectionWidth 4
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 199 residues in model #1.2 to IUPAC-IUB
standards.
Opened (LIVE) MDFF potential as #1.1.1.12, grid size 46,44,42, pixel
0.579,0.578,0.581, shown at level 0.56, step 1, values float32
Done loading forcefield
> isolde set simFidelityMode Highest/Slowest
ISOLDE: setting sim fidelity mode to Highest/Slowest
nonbonded_cutoff_distance = 1.700000
use_gbsa = True
gbsa_cutoff = 2.000000
> addh
Summary of feedback from adding hydrogens to 0017-01_refmacat.pdb #1.2
---
notes | Termini for 0017-01_refmacat.pdb (#1.2) chain A determined from SEQRES
records
Termini for 0017-01_refmacat.pdb (#1.2) chain B determined from SEQRES records
Termini for 0017-01_refmacat.pdb (#1.2) chain C determined from SEQRES records
Termini for 0017-01_refmacat.pdb (#1.2) chain D determined from SEQRES records
Termini for 0017-01_refmacat.pdb (#1.2) chain E determined from SEQRES records
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A SER -1, /B MET 1, /C MET
1, /D SER 0, /E MET 1, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1, /K
MET 1, /L MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 283, /B LEU 280, /C ASP
278, /D PHE 284, /E LEU 283, /F GLN 282, /G PHE 284, /H ASN 281, /I LEU 280,
/J LEU 283, /K ASN 281, /L GLN 282
Chain-final residues that are not actual C termini:
Missing OXT added to C-terminal residue /A LEU 283
Missing OXT added to C-terminal residue /B LEU 280
Missing OXT added to C-terminal residue /C ASP 278
Missing OXT added to C-terminal residue /D PHE 284
Missing OXT added to C-terminal residue /E LEU 283
7 messages similar to the above omitted
6545 hydrogen bonds
28955 hydrogens added
> select #1/B,A,D
13083 atoms, 13192 bonds, 853 residues, 1 model selected
> select #1/B,A,D,C
17352 atoms, 17497 bonds, 1132 residues, 1 model selected
> isolde sim start /A-D
Loading residue template for DMS from internal database
Loading residue template for ICT from internal database
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: stopped sim
> addh #1.2
Summary of feedback from adding hydrogens to 0017-01_refmacat.pdb #1.2
---
notes | Termini for 0017-01_refmacat.pdb (#1.2) chain A determined from SEQRES
records
Termini for 0017-01_refmacat.pdb (#1.2) chain B determined from SEQRES records
Termini for 0017-01_refmacat.pdb (#1.2) chain C determined from SEQRES records
Termini for 0017-01_refmacat.pdb (#1.2) chain D determined from SEQRES records
Termini for 0017-01_refmacat.pdb (#1.2) chain E determined from SEQRES records
7 messages similar to the above omitted
Chain-initial residues that are actual N termini: /A SER -1, /B MET 1, /C MET
1, /D SER 0, /E MET 1, /F MET 1, /G MET 1, /H MET 1, /I MET 1, /J MET 1, /K
MET 1, /L MET 1
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: /A LEU 283, /B LEU 280, /C ASP
278, /D PHE 284, /E LEU 283, /F GLN 282, /G PHE 284, /H ASN 281, /I LEU 280,
/J LEU 283, /K ASN 281, /L GLN 282
Chain-final residues that are not actual C termini:
5109 hydrogen bonds
3 hydrogens added
> select #1/B,A,D,C
17353 atoms, 17498 bonds, 1132 residues, 1 model selected
> isolde sim start /A-D
ISOLDE: started sim
> struts first
Missing or invalid "atoms" argument: invalid atoms specifier
> struts sel first
Expected a keyword
> struts s
Missing or invalid "atoms" argument: invalid atoms specifier
> struts
Missing or invalid "atoms" argument: empty atom specifier
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 15 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /I:174
ISOLDE: started sim
> isolde pepflip /I:173
> isolde pepflip /I:174
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip /I:174
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde pepflip /L:188
ISOLDE: started sim
> isolde pepflip /L:188
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start /E:195
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /F:2
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start /E:265
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> open 1xg4
1xg4 title:
Crystal Structure of the C123S 2-Methylisocitrate Lyase Mutant from
Escherichia coli in complex with the inhibitor isocitrate [more info...]
Chain information for 1xg4 #2
---
Chain | Description | UniProt
A B C D | Probable methylisocitrate lyase | PRPB_ECOLI 2-296
Non-standard residues in 1xg4 #2
---
ICT — isocitric acid
MG — magnesium ion
> mmaker #2 to #1/H
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain H (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 957.5
RMSD between 273 pruned atom pairs is 0.719 angstroms; (across all 279 pairs:
0.899)
> hide sel cartoons
> show sel atoms
> select #2
9718 atoms, 8866 bonds, 18 pseudobonds, 2131 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
> show sel atoms
> select #2fit #2/D in #1.1.1
Expected an objects specifier or a keyword
> select clear
> hide #!2 models
> isolde sim start #1.2/H:189
ISOLDE: started sim
> isolde pepflip #1.2/H:189
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/K:131
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/L:183
ISOLDE: started sim
> isolde pepflip #1.2/L:183
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/K:188
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> show #!2 models
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/G:198
ISOLDE: started sim
> mmaker #2 to #1/G
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain G (#1.2) with 1xg4, chain A (#2),
sequence alignment score = 966.3
RMSD between 269 pruned atom pairs is 0.624 angstroms; (across all 282 pairs:
1.252)
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/K:198
ISOLDE: started sim
> isolde pepflip #1.2/K:198
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> mmaker #2 to #1/
> matchmaker #2 to #1/
Invalid "to" argument: only initial part "#1" of atom specifier valid
> mmaker #2 to #1/K
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain K (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 956.9
RMSD between 272 pruned atom pairs is 0.674 angstroms; (across all 279 pairs:
0.862)
> hide #!1 models
> show #!1 models
> isolde sim start #1.2/K:198
ISOLDE: started sim
> isolde pepflip #1.2/K:198
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/D:198
ISOLDE: started sim
> isolde pepflip #1.2/D:198
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/D:198
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde pepflip #1.2/C:185
ISOLDE: started sim
> isolde pepflip #1.2/C:185
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> mmaker #2 to #1/C
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain C (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 940.3
RMSD between 272 pruned atom pairs is 0.630 angstroms; (across all 278 pairs:
0.848)
> hide #!2 models
> isolde sim start #1.2/C:184
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/J:118
ISOLDE: started sim
> mmaker #2 to #1/J
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain J (#1.2) with 1xg4, chain C (#2),
sequence alignment score = 963.9
RMSD between 268 pruned atom pairs is 0.763 angstroms; (across all 283 pairs:
1.556)
> show #!2 models
> isolde sim pause
> hide #!1 models
> mmaker #2/A to #1/J
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain J (#1.2) with 1xg4, chain A (#2),
sequence alignment score = 962.7
RMSD between 278 pruned atom pairs is 0.705 angstroms; (across all 282 pairs:
0.850)
> show #!1 models
> hide #!1 models
> show #!1 models
> select #1.2/S:978
3 atoms, 2 bonds, 1 residue, 1 model selected
> select #1.2/S:978,1181
6 atoms, 4 bonds, 2 residues, 1 model selected
> delete sel
Sim termination reason: coord length mismatch
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/J:118
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/J:116
ISOLDE: started sim
> hide #!2 models
> show #!2 models
> isolde pepflip #1.2/J:116
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!2 models
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/E:5
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/J:184
ISOLDE: started sim
> isolde pepflip #1.2/J:184
> show #!2 models
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/D:275
ISOLDE: started sim
> isolde pepflip #1.2/D:276
> isolde pepflip #1.2/D:275
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> hide #!1 models
> show #!1 models
> hide #!2 models
> show #!2 models
> mmaker #2 to #1/D
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain D (#1.2) with 1xg4, chain C (#2),
sequence alignment score = 974.5
RMSD between 271 pruned atom pairs is 0.715 angstroms; (across all 284 pairs:
1.574)
> isolde sim start #1.2/D:279
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/F:184
ISOLDE: started sim
> mmaker #2 to #1/F
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain F (#1.2) with 1xg4, chain A (#2),
sequence alignment score = 955.7
RMSD between 275 pruned atom pairs is 0.670 angstroms; (across all 282 pairs:
0.871)
> hide #!2 models
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/L:115
ISOLDE: started sim
> mmaker #2 to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain L (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 942.5
RMSD between 263 pruned atom pairs is 0.777 angstroms; (across all 279 pairs:
2.729)
> show #!2 models
> hide #!2 models
> show #!2 models
> mmaker #2/A to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain L (#1.2) with 1xg4, chain A (#2),
sequence alignment score = 937.1
RMSD between 267 pruned atom pairs is 0.781 angstroms; (across all 282 pairs:
2.709)
> mmaker #2/B to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain L (#1.2) with 1xg4, chain B (#2),
sequence alignment score = 934.1
RMSD between 266 pruned atom pairs is 0.786 angstroms; (across all 282 pairs:
2.713)
> mmaker #2/C to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain L (#1.2) with 1xg4, chain C (#2),
sequence alignment score = 937.1
RMSD between 264 pruned atom pairs is 0.808 angstroms; (across all 282 pairs:
2.206)
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> select #1.2/S:1268
3 atoms, 2 bonds, 1 residue, 1 model selected
> delete sel
> isolde sim start #1.2/L:115
ISOLDE: started sim
> hide #!2 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> mmaker #2/D to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain L (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 942.5
RMSD between 263 pruned atom pairs is 0.777 angstroms; (across all 279 pairs:
2.724)
> show #!2 models
> mmaker #2/E to #1/L
No molecules/chains to match specified
> mmaker #2 to #1/L
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain L (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 942.5
RMSD between 263 pruned atom pairs is 0.777 angstroms; (across all 279 pairs:
2.724)
> ui tool show "Ramachandran Plot"
> hide #!2 models
> mmaker #2 to #1/I
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain I (#1.2) with 1xg4, chain C (#2),
sequence alignment score = 958
RMSD between 263 pruned atom pairs is 0.746 angstroms; (across all 280 pairs:
1.670)
> show #!2 models
> hide #!2 models
> isolde sim start #1.2/I:186
ISOLDE: started sim
> isolde pepflip #1.2/I:186
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/I:188
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/A:182
ISOLDE: started sim
> mmaker #2 to #1/A
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain A (#1.2) with 1xg4, chain C (#2),
sequence alignment score = 972.5
RMSD between 269 pruned atom pairs is 0.728 angstroms; (across all 284 pairs:
1.555)
> show #!2 models
> isolde pepflip #1.2/A:182
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> isolde sim start #1.2/A:182
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> mmaker #2 to #1/E
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 0017-01_refmacat.pdb, chain E (#1.2) with 1xg4, chain D (#2),
sequence alignment score = 958.5
RMSD between 271 pruned atom pairs is 0.655 angstroms; (across all 279 pairs:
0.862)
> isolde sim start #1.2/E:117
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> isolde sim start #1.2/E:116
ISOLDE: started sim
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback
self.ff(*self.ff_args)
File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1531, in
_update_coordinates_and_repeat
self.atoms.coords = th.coords
^^^^^^^^^
File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 103, in coords
return self.smoothed_coords
^^^^^^^^^^^^^^^^^^^^
RuntimeError: Error invoking kernel: CUDA_ERROR_ILLEGAL_ADDRESS (700)
Error processing trigger "new frame":
RuntimeError: Error invoking kernel: CUDA_ERROR_ILLEGAL_ADDRESS (700)
File "/home/alphafold/.local/share/ChimeraX/1.7/lib/python3.11/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 103, in coords
return self.smoothed_coords
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> isolde sim stop discardTo start
> isolde sim pause
> isolde sim stop discardTo start
Sim termination reason: None
reverting to start
Updating bulk solvent parameters...
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> ui tool show "Ramachandran Plot"
> isolde sim start #1.2/C:117
Launching using CUDA failed with the below message. Falling back to using
OpenCL.
No compatible CUDA device is available
ISOLDE: started sim
> isolde pepflip #1.2/C:116
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.2
Locale: en_GB.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=:1
Manufacturer: To Be Filled By O.E.M.
Model: To Be Filled By O.E.M.
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: 125Gi 64Gi 51Gi 386Mi 10Gi 60Gi
Swap: 15Gi 15Gi 18Mi
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
Installed Packages:
alabaster: 0.7.13
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: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
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-Clipper: 0.22.3
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
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-ISOLDE: 1.7
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
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: 1.5.13
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: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PhenixUI: 1.2.2
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: 1.12.3
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: 1.33.2
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: 0.2.0
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: 4.47.0
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: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
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: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
pprintpp: 0.4.0
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: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
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: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 15 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 , 15 months ago
| Cc: | added |
|---|---|
| Resolution: | → duplicate |
| Status: | accepted → closed |
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