Opened 23 months ago

Closed 23 months ago

#10434 closed defect (can't reproduce)

Crash in Open→File dialog

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI 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-5.14.0-362.8.1.el9_3.x86_64-x86_64-with-glibc2.34
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Bus error

Thread 0x00007f49177fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4917fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4934ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/selectors.py", line 416 in select
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49357fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4935ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49367fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4936ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49377fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4937fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4954ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49557fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4955ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49567fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4956ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49577fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4957fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4974ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49757fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4975ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49767fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4976ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49777fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4977fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4994ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49957fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4995ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49967fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4996ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49977fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4997fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b4ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b57fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b5ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b67fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b6ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b77fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49b7fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d4ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d57fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d5ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d67fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d6ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d77fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49d7fff640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49f4ff9640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49f57fa640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49f5ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f49f67fc640 (most recent call first):
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Thread 0x00007f49f6ffd640 (most recent call first):
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Thread 0x00007f49f77fe640 (most recent call first):
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Thread 0x00007f49f7fff640 (most recent call first):
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Thread 0x00007f4a14ff9640 (most recent call first):
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Thread 0x00007f4a157fa640 (most recent call first):
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Thread 0x00007f4a15ffb640 (most recent call first):
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Thread 0x00007f4a167fc640 (most recent call first):
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Thread 0x00007f4a16ffd640 (most recent call first):
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Thread 0x00007f4a177fe640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a17fff640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a34ff9640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a357fa640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a35ffb640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a367fc640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a36ffd640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
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Thread 0x00007f4a377fe640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a37fff640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a54ff9640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a557fa640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a55ffb640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a567fc640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a56ffd640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a577fe640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a57fff640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a74ff9640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a757fa640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a75ffb640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a767fc640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a76ffd640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a777fe640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a77fff640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a94ff9640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a957fa640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a95ffb640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a967fc640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a96ffd640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a977fe640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4a97fff640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab4ff9640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab57fa640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab5ffb640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab67fc640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab6ffd640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab77fe640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ab7fff640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ad4ff9640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ad57fa640 (most recent call first):
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  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ad5ffb640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ad67fc640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ad6ffd640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f4ad77fe640 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 910 in run
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f4caa04b2c0 (most recent call first):
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 135 in show_open_file_dialog
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/open_command/dialog.py", line 107 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 892 in init
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1043 in 
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /panfs/home/aalam/aalam/2022_09_26_B1sapoapo/phenix/RealSpaceRefine_13/B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb

Chain information for
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb #1  
---  
Chain | Description  
A | No description available  
  

> set bgColor white

> color bychain

> lighting soft

> lighting shadows true intensity 0.5

> graphics silhouettes true

> open
> /panfs/home/aalam/aalam/2022_10_06_B1sapozos/phenix/RealSpaceRefine_15/B1sapozos_RSR15.pdb

Chain information for B1sapozos_RSR15.pdb #2  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #!2 to #1

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
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb,
chain A (#1) with B1sapozos_RSR15.pdb, chain A (#2), sequence alignment score
= 4951.2  
RMSD between 379 pruned atom pairs is 0.979 angstroms; (across all 1081 pairs:
10.194)  
  

> matchmaker #!2 to #1

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
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb,
chain A (#1) with B1sapozos_RSR15.pdb, chain A (#2), sequence alignment score
= 4951.2  
RMSD between 379 pruned atom pairs is 0.979 angstroms; (across all 1081 pairs:
10.194)  
  

> open
> /panfs/home/aalam/aalam/20230614_B1sapoTAX_ATP/RealSpaceRefine_5/B1sapoTaxATP_RSR5.pdb

Chain information for B1sapoTaxATP_RSR5.pdb #3  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #!2-3 to #1

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
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb,
chain A (#1) with B1sapozos_RSR15.pdb, chain A (#2), sequence alignment score
= 4951.2  
RMSD between 379 pruned atom pairs is 0.979 angstroms; (across all 1081 pairs:
10.194)  
  
Matchmaker
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb,
chain A (#1) with B1sapoTaxATP_RSR5.pdb, chain A (#3), sequence alignment
score = 4985.5  
RMSD between 374 pruned atom pairs is 1.137 angstroms; (across all 1081 pairs:
13.483)  
  

> matchmaker #!2-3 to #1

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
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb,
chain A (#1) with B1sapozos_RSR15.pdb, chain A (#2), sequence alignment score
= 4951.2  
RMSD between 379 pruned atom pairs is 0.979 angstroms; (across all 1081 pairs:
10.194)  
  
Matchmaker
B1sapoapo_RSR10-1_real_space_refined_011-coot-0_real_space_refined_013.pdb,
chain A (#1) with B1sapoTaxATP_RSR5.pdb, chain A (#3), sequence alignment
score = 4985.5  
RMSD between 374 pruned atom pairs is 1.137 angstroms; (across all 1081 pairs:
13.483)  
  

> hide atoms

> hide #!2 models

> dssp

> hide #1.1 models

> hide #2.1 models

> hide #3.1 models

> select #1/A

8508 atoms, 8678 bonds, 2 pseudobonds, 1086 residues, 2 models selected  

> select #1/A,1

8508 atoms, 8678 bonds, 2 pseudobonds, 1086 residues, 2 models selected  

> select #1/A:1

Nothing selected  

> select #1/A:1-400

2633 atoms, 2692 bonds, 1 pseudobond, 339 residues, 2 models selected  

> select #1/A:983

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select #1/A:983,310

23 atoms, 23 bonds, 2 residues, 1 model selected  

> select #1/A:983,310,990,770,303,838,725,721,728,987

96 atoms, 91 bonds, 10 residues, 1 model selected  

> show sel atoms

> select #2/A:983,310,990,770,303,838,725,721,728,987

96 atoms, 91 bonds, 10 residues, 1 model selected  

> show #!1,3 atoms

> hide #!1,3 atoms

> select #1-3/A:983,310,990,770,303,838,725,721,728,987

288 atoms, 273 bonds, 30 residues, 3 models selected  

> show sel & #!1,3 atoms

> select clear

> select #1-3

27636 atoms, 28234 bonds, 6 pseudobonds, 3467 residues, 6 models selected  

> hide sel & #!1,3 cartoons

> select clear

> select #1-3/A:983,310,990,770,303,838,725,721,728,987

288 atoms, 273 bonds, 30 residues, 3 models selected  

> show sel & #!1,3 atoms

> show #!2 models

> hide #!2 models

> show #!2 models

> hide sel cartoons

> select #1-3

27636 atoms, 28234 bonds, 6 pseudobonds, 3467 residues, 6 models selected  

> hide sel cartoons

> select clear

> select #2/A:983,310,990,770,303,838,725,721,728,987

96 atoms, 91 bonds, 10 residues, 1 model selected  

> show sel atoms

> select clear

> select #1-3/A:983,310,990,770,303,838,725,721,728,987

288 atoms, 273 bonds, 30 residues, 3 models selected  

> color sel byhetero

> select clear

> select #1-3/1-100

Nothing selected  

> select #1-3/A:1-100

1295 atoms, 1322 bonds, 2 pseudobonds, 167 residues, 5 models selected  

> show sel cartoons

> hide sel cartoons


===== Log before crash end =====

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.5 (Core Profile) Mesa 23.1.4
OpenGL renderer: llvmpipe (LLVM 16.0.6, 256 bits)
OpenGL vendor: Mesa

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=unspecified
DESKTOP_SESSION=
XDG_SESSION_DESKTOP=
XDG_CURRENT_DESKTOP=MATE
DISPLAY=:1
VGL_DISPLAY=/dev/dri/card1
Manufacturer: Dell Inc.
Model: DSS8440
OS: Rocky Linux 9.3 Blue Onyx
Architecture: 64bit ELF
Virtual Machine: none
CPU: 96 Intel(R) Xeon(R) Gold 6248R CPU @ 3.00GHz
Cache Size: 36608 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           375Gi        10Gi       175Gi        76Mi       192Gi       365Gi
	Swap:          4.0Gi       559Mi       3.5Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: Matrox Electronics Systems Ltd. Integrated Matrox G200eW3 Graphics Controller [102b:0536] (rev 04)	
	DeviceName: Embedded Video	
	Subsystem: Dell Device [1028:088d]

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    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: 1.1.1
    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: 1.2.1
    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-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 23 months ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in Open→File dialog

comment:2 by Eric Pettersen, 23 months ago

Resolution: → can't reproduce
Status: accepted → closed

Not a lot of clues about what exactly went wrong. There were a lot of threads running.

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