Opened 3 months ago

Closed 3 months ago

#18310 closed defect (duplicate)

Crash on Mac waking from sleep

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Window Toolkit Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x0000000549e83000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000548e77000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000547e6b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000546e5f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000545e53000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000544e47000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000543e3b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000542e2f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000541e23000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000540e17000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000053fe0b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000053edff000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000053ddf3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000053cde7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000051c807000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000052cc0f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000052bc03000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000052abf7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000529beb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000528bdf000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000527bd3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000526bc7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000525bbb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000524baf000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000523ba3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000522b97000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000521b8b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000520b7f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000051fb73000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000051d92b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000050674b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000050573f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000504733000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000503727000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000050271b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x000000050170f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x0000000500703000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004ff6f7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004fe6eb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004fd6df000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004fc6d3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004fb6c7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004fa6bb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004f96af000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004e639b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004ca24b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c923f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c8233000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c7227000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c621b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c520f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c4203000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c31f7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c21eb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c11df000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004c01d3000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004bf1c7000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004be1bb000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004bc08b000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00000004bb07f000 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x0000000203801f00 (most recent call first):
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 315 in event_loop
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1003 in init
  File "/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.dssp._dssp, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.connect_structure._cs, chimerax.atom_search.ast, chimerax.chem_group._chem_group, psutil._psutil_osx, psutil._psutil_posix, chimerax.md_crds._gromacs, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, PIL._webp, chimerax.coulombic._esp (total: 72)


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fault"},"pc":{"value":6801802188},"far":{"value":0}}},{"id":13178099,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":202},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":203},{"imageOffset":2309256,"symbol":"PyThread_acquire_lock_timed","symbolLocation":412,"imageIndex":1},{"imageOffset":13260,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":220,"imageIndex":78},{"imageOffset":12360,"symbol":"_queue_SimpleQueue_get","symbolLocation":224,"imageIndex":78},{"imageOffset":1008200,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":100,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":1799532,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":65272,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611492,"symbol":"method_vectorcall","symbolLocation":388,"imageIndex":1},{"imageOffset":2848544,"symbol":"thread_run","symbolLocation":200,"imageIndex":1},{"imageOffset":2308224,"symbol":"pythread_wrapper","symbolLocation":48,"imageIndex":1},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":203},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":203}],"threadState":{"x":[{"value":260},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":20571269496},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8665767776},{"value":0},{"value":105553446743864},{"value":105553446743816},{"value":20571271392},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":0},{"value":5241164524}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6802059488},"cpsr":{"value":1610616832},"fp":{"value":20571269616},"sp":{"value":20571269472},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6801802188},"far":{"value":0}}},{"id":13214890,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":202},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":203},{"imageOffset":2309256,"symbol":"PyThread_acquire_lock_timed","symbolLocation":412,"imageIndex":1},{"imageOffset":13260,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":220,"imageIndex":78},{"imageOffset":12360,"symbol":"_queue_SimpleQueue_get","symbolLocation":224,"imageIndex":78},{"imageOffset":1008200,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":100,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":1799532,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":65272,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611492,"symbol":"method_vectorcall","symbolLocation":388,"imageIndex":1},{"imageOffset":2848544,"symbol":"thread_run","symbolLocation":200,"imageIndex":1},{"imageOffset":2308224,"symbol":"pythread_wrapper","symbolLocation":48,"imageIndex":1},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":203},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":203}],"threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":21042407800},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8665767776},{"value":0},{"value":105553379651896},{"value":105553379651848},{"value":21042409696},{"value":0},{"value":0},{"value":0},{"value":1},{"value":256},{"value":0},{"value":5238953484}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6802059488},"cpsr":{"value":1610616832},"fp":{"value":21042407920},"sp":{"value":21042407776},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6801802188},"far":{"value":0}}},{"id":13214891,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":202},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":203},{"imageOffset":2309256,"symbol":"PyThread_acquire_lock_timed","symbolLocation":412,"imageIndex":1},{"imageOffset":13260,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":220,"imageIndex":78},{"imageOffset":12360,"symbol":"_queue_SimpleQueue_get","symbolLocation":224,"imageIndex":78},{"imageOffset":1008200,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":100,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":1799532,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":65272,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611492,"symbol":"method_vectorcall","symbolLocation":388,"imageIndex":1},{"imageOffset":2848544,"symbol":"thread_run","symbolLocation":200,"imageIndex":1},{"imageOffset":2308224,"symbol":"pythread_wrapper","symbolLocation":48,"imageIndex":1},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":203},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":203}],"threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":21364402552},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8665767776},{"value":0},{"value":105553379651896},{"value":105553379651848},{"value":21364404448},{"value":0},{"value":0},{"value":0},{"value":0},{"value":512},{"value":0},{"value":5238953484}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6802059488},"cpsr":{"value":1610616832},"fp":{"value":21364402672},"sp":{"value":21364402528},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6801802188},"far":{"value":0}}},{"id":13214892,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":202},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":203},{"imageOffset":2309256,"symbol":"PyThread_acquire_lock_timed","symbolLocation":412,"imageIndex":1},{"imageOffset":13260,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":220,"imageIndex":78},{"imageOffset":12360,"symbol":"_queue_SimpleQueue_get","symbolLocation":224,"imageIndex":78},{"imageOffset":1008200,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":100,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":1799532,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":65272,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611492,"symbol":"method_vectorcall","symbolLocation":388,"imageIndex":1},{"imageOffset":2848544,"symbol":"thread_run","symbolLocation":200,"imageIndex":1},{"imageOffset":2308224,"symbol":"pythread_wrapper","symbolLocation":48,"imageIndex":1},{"imageOffset":27660,"symbol":"_pthread_start","symbolLocation":136,"imageIndex":203},{"imageOffset":7040,"symbol":"thread_start","symbolLocation":8,"imageIndex":203}],"threadState":{"x":[{"value":4},{"value":0},{"value":0},{"value":0},{"value":0},{"value":160},{"value":0},{"value":0},{"value":21381228920},{"value":0},{"value":0},{"value":2},{"value":2},{"value":0},{"value":0},{"value":0},{"value":305},{"value":8665767776},{"value":0},{"value":105553379651896},{"value":105553379651848},{"value":21381230816},{"value":0},{"value":0},{"value":0},{"value":0},{"value":768},{"value":0},{"value":5238953484}],"flavor":"ARM_THREAD_STATE64","lr":{"value":6802059488},"cpsr":{"value":1610616832},"fp":{"value":21381229040},"sp":{"value":21381228896},"esr":{"value":1442840704,"description":" Address size fault"},"pc":{"value":6801802188},"far":{"value":0}}},{"id":13214893,"frames":[{"imageOffset":17356,"symbol":"__psynch_cvwait","symbolLocation":8,"imageIndex":202},{"imageOffset":28896,"symbol":"_pthread_cond_wait","symbolLocation":984,"imageIndex":203},{"imageOffset":2309256,"symbol":"PyThread_acquire_lock_timed","symbolLocation":412,"imageIndex":1},{"imageOffset":13260,"symbol":"_queue_SimpleQueue_get_impl","symbolLocation":220,"imageIndex":78},{"imageOffset":12360,"symbol":"_queue_SimpleQueue_get","symbolLocation":224,"imageIndex":78},{"imageOffset":1008200,"symbol":"cfunction_vectorcall_FASTCALL_KEYWORDS_METHOD","symbolLocation":100,"imageIndex":1},{"imageOffset":1788292,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":54032,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":1799532,"symbol":"_PyEval_EvalFrameDefault","symbolLocation":65272,"imageIndex":1},{"imageOffset":1811404,"symbol":"_PyEval_Vector","symbolLocation":156,"imageIndex":1},{"imageOffset":611492,"symbol":"method_vectorcall","symbolLocation":388,"imageIndex":1},{"imageOffset":2848544,"symbol":"thread_run","symbolLocation":200,"imageIndex":1},
[deleted to fit within ticket limits]



> show #6 models

> select #4.1/A:125

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select add #6/A:125

24 atoms, 22 bonds, 2 residues, 2 models selected  

> show sel atoms

> color sel byhetero

> hide #6 models

> show #6 models

> hide #6 models

The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.  

> show #2 models

> hide #!4 models

> hide #4.1 models

> view

> show #2:ARG

> show #2:LYS

> show #2:GLU

> show #2:ASP

> select #2:SER

495 atoms, 456 bonds, 45 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 495 atom styles  

> graphics silhouettes true

> graphics silhouettes false

> lighting soft

> lighting full

> lighting soft

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/SLC7A4_TM_Arginine/pr200ns_run1_whole_nojump_center_rotxyz-
> transxyz.pdb"

Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/SLC7A4_TM_Arginine/pr200ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
pr200ns_run1_whole_nojump_center_rotxyz-transxyz.pdb title:  
SLC7A4-Leu in POPC-Cholesterol in water t= 200000.00000 step= 100000000 [more
info...]  
  
Chain information for pr200ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #9  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in pr200ns_run1_whole_nojump_center_rotxyz-transxyz.pdb
#9  
---  
ACE — (ACE)  
CHL1 — (CHL1)  
CL — (CL)  
NA — (NA)  
NME — (NME)  
POPC — (popc)  
SOL — (SOL)  
ZR — (ZR)  
  

> hide #2 models

> view

> select #9:ZR

27 atoms, 26 bonds, 1 residue, 1 model selected  

> hide #9 atoms

> select #9:ZR

27 atoms, 26 bonds, 1 residue, 1 model selected  

> show sel atoms

> select sel : show sel atoms

> view sel

> ~display HC

> select #9:ZR

27 atoms, 26 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0
> twoColors true slopColor #ff9300 select true reveal true

17 hydrogen bonds found  
9 strict hydrogen bonds found  

> hide sel cartoons

> label sel

> label height 0.5

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select clear

> select add #9@@serial_number=29722

2 atoms, 2 residues, 1 model selected  

> select add #9/B:594@C

3 atoms, 3 residues, 1 model selected  

> select add #9@@serial_number=63161

4 atoms, 4 residues, 1 model selected  

> select add #9@@serial_number=34282

6 atoms, 6 residues, 1 model selected  

> select add #9@@serial_number=29141

8 atoms, 8 residues, 1 model selected  

> select add #9@@serial_number=90556

9 atoms, 9 residues, 1 model selected  

> select add #9@@serial_number=52898

11 atoms, 11 residues, 1 model selected  

> select add #9@@serial_number=40903

13 atoms, 13 residues, 1 model selected  

> select add #9@@serial_number=42401

15 atoms, 15 residues, 1 model selected  

> select add #9@@serial_number=94830

16 atoms, 16 residues, 1 model selected  

> select add #9@@serial_number=57339

18 atoms, 18 residues, 1 model selected  

> select add #9@@serial_number=90554

19 atoms, 18 residues, 1 model selected  

> select up

864 atoms, 846 bonds, 18 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0
> twoColors true slopColor #ff9300 select true reveal true

92 hydrogen bonds found  
58 strict hydrogen bonds found  

> select clear

> hide #9 cartoons

> select clear

> hide #9.2 models

> show #9.2 models

> hide #9.1 models

> show #9.1 models

> camera mono

> camera ortho

> graphics silhouettes true

> hide #9.1 models

> hide #9.2 models

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/SLC7A4_TM_Arginine/pr200ns_run1_whole_nojump_center_rotxyz-
> transxyz.xtc"

Replaced existing frames of pr200ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb #9 with 4001 new frames  

> show #9.1 models

> hide #9.1 models

> show #9.1 models

> hide #9.1 models

> color #9:ZR magenta

> color #9:ZR byhetero

swapaa cannot align to residues pr200ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb #9/? SOL 1207 which has fewer than 3 backbone atoms (N, C, CA)  
swapaa cannot align to residues pr200ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb #9/? SOL 2279 which has fewer than 3 backbone atoms (N, C, CA)  

> swapaa mousemode #9/A:336 SER

> close #9

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_leucine/pr1000ns/pr1000ns.gro"

Chain information for AtCAT4-Leu in POPC-Cholesterol in water #9  
---  
Chain | Description  
? | No description available  
  

> hide #9:POPC,CHL1

> hide #9 atoms

> select #9:ZL

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> view sel

> select sel : show sel & #9 atoms

> hide #9 models

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/AtCAT4_leucine/pr1000ns/pr1000ns_whole_nojump_center_rotxyz-
> transxyz_skip10.xtc"

Replaced existing frames of AtCAT4-Leu in POPC-Cholesterol in water #9 with
2001 new frames  

> select add #4

4565 atoms, 4571 bonds, 670 residues, 3 models selected  

> select subtract #4

357 atoms, 243 bonds, 114 residues, 1 model selected  

> select add #9

158053 atoms, 124008 bonds, 35006 residues, 1 model selected  

> view

> show #9 models

> show sel cartoons

> view

> hide :9:SOL

> hide :9:SOL,CL,NA

> select clear

> select #9/?:581@CA

1 atom, 1 residue, 1 model selected  

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> select sel : show sel atoms

> ~display HC

> view sel

> close #9

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/pr1000ns/pr1000ns_whole_nojump_center_rotxyz-
> transxyz.pdb"

Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/pr1000ns/pr1000ns_whole_nojump_center_rotxyz-
transxyz.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
pr1000ns_whole_nojump_center_rotxyz-transxyz.pdb title:  
SLC7A4-Leu in POPC-Cholesterol in water t= 1000000.00000 step= 500000000 [more
info...]  
  
Chain information for pr1000ns_whole_nojump_center_rotxyz-transxyz.pdb #9  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in pr1000ns_whole_nojump_center_rotxyz-transxyz.pdb #9  
---  
ACE — (ACE)  
CHL1 — (CHL1)  
CL — (CL)  
NA — (NA)  
NME — (NME)  
POPC — (popc)  
SOL — (SOL)  
ZR — (ZR)  
  

> select #9:ZR

27 atoms, 26 bonds, 1 residue, 1 model selected  

> view sel

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/setup/step6.8_equilibration.gro"

Chain information for SLC7A4-Leu in POPC-Cholesterol in water #10  
---  
Chain | Description  
? | No description available  
  

> hide #9 models

> select #10/?:252

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

> show sel atoms

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/SLC7A4_homology_model_arginine_att2/setup/system_solvated_ions.gro"

Chain information for SLC7A4-Leu in POPC-Cholesterol in water #11  
---  
Chain | Description  
? | No description available  
  

> matchmaker #11 to #10

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 SLC7A4-Leu in POPC-Cholesterol in water, chain (blank) (#10) with
SLC7A4-Leu in POPC-Cholesterol in water, chain (blank) (#11), sequence
alignment score = 2615.7  
RMSD between 370 pruned atom pairs is 1.140 angstroms; (across all 555 pairs:
7.002)  
  

> hide #10 models

> hide #11 models

> show #9 models

> close #9-11

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run1/pr200ns_run1.gro"

Chain information for AtCAT4-Arg in POPC-Cholesterol in water #9  
---  
Chain | Description  
? | No description available  
  

> select :ZR

27 atoms, 26 bonds, 1 residue, 1 model selected  

> view sel

> select #9/?:243

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

> show sel atoms

> select clear

> select #9/?:327

11 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel atoms

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run2/pr200ns_run2.gro"

Chain information for AtCAT4-Arg in POPC-Cholesterol in water #10  
---  
Chain | Description  
? | No description available  
  

> matchmaker #10 to #9

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 AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with
AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#10), sequence
alignment score = 2715.2  
RMSD between 410 pruned atom pairs is 1.022 angstroms; (across all 551 pairs:
2.140)  
  

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run3/pr200ns_run3_whole_nojump_center_rotxyz-
> transxyz.pdb"

Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/AtCAT4_arginine/pr200ns_reps/run3/pr200ns_run3_whole_nojump_center_rotxyz-
transxyz.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb title:  
AtCAT4-Arg in POPC-Cholesterol in water t= 200000.00000 step= 100000000 [more
info...]  
  
Chain information for pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb #11  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb
#11  
---  
ACE — (ACE)  
CHL1 — (CHL1)  
CL — (CL)  
NA — (NA)  
NME — (NME)  
POPC — (popc)  
SOL — (SOL)  
ZR — (ZR)  
  

> matchmaker #11 to #9

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 AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with
pr200ns_run3_whole_nojump_center_rotxyz-transxyz.pdb, chain A (#11), sequence
alignment score = 2690  
RMSD between 426 pruned atom pairs is 1.022 angstroms; (across all 551 pairs:
2.015)  
  

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/AtCAT4_arginine/equilibration/step6.8_equilibration.gro"

Chain information for AtCAT4-Arg in POPC-Cholesterol in water #12  
---  
Chain | Description  
? | No description available  
  

> matchmaker #12 to #9

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 AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with
AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#12), sequence
alignment score = 2549  
RMSD between 378 pruned atom pairs is 1.139 angstroms; (across all 551 pairs:
5.844)  
  

> close #12

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_arginine/charmm-
> gui-0619450548/gromacs/step6.0_minimization.gro"

Chain information for AtCAT4-Arg in POPC-Cholesterol in water #12  
---  
Chain | Description  
? | No description available  
  

> matchmaker #12 to #9

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 AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#9) with
AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#12), sequence
alignment score = 2526.8  
RMSD between 337 pruned atom pairs is 1.109 angstroms; (across all 551 pairs:
5.776)  
  

> hide #9 models

> hide #10 models

> hide #11 models

> open "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Ornithine/250630 -
> newmodel_TM1 induced
> fit/RealSpaceRefine_72/ORN_real_space_refined_063_mapJ510-coot-sn.pdb"

Chain information for ORN_real_space_refined_063_mapJ510-coot-sn.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> matchmaker #13 to #12

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 AtCAT4-Arg in POPC-Cholesterol in water, chain (blank) (#12) with
ORN_real_space_refined_063_mapJ510-coot-sn.pdb, chain A (#13), sequence
alignment score = 2428.2  
RMSD between 439 pruned atom pairs is 0.864 angstroms; (across all 506 pairs:
1.659)  
  

> dssp #13

> hide #12 models

> show #12 models

> select #12/?:47

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> select #13/A:47

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> dssp #12

> hide #12 models

> show #9 models

> select #9/?:47

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #10 models

> hide #9 models

> select #10/?:47

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide #10 models

> show #11 models

> select #11/A:48

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select #11/A:48

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select clear

> select #11/A:47

21 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #13:HOH

> select #13/A:117

12 atoms, 12 bonds, 1 residue, 1 model selected  

> show sel atoms

> close #2,4-6,9-12#1,3,7-8,13

> open "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Figure
> 1/revised_250722/1e/Fig1e_CAT4-ORN_updated_unsharpenedmap.cxs"

Opened cryosparc_P60_J427_008_volume_map_sharp.mrc as #6, grid size
288,288,288, pixel 0.835, shown at level 0.21, step 1, values float32  
Opened cryosparc_P60_J510_006_volume_map_sharp.mrc as #9, grid size
576,576,576, pixel 0.417, shown at level 0.03, step 1, values float32  
Opened cryosparc_P60_J510_005_volume_map.mrc as #10, grid size 576,576,576,
pixel 0.417, shown at level 0.008, step 1, values float32  
opened ChimeraX session  

> close #1,3-4#2,5-6

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> hide #!8 models

> show #!8 models

> show #!7 models

> show #7 cartoons

> hide #8 atoms

> delete labels

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete label

Missing or invalid "atoms" argument: invalid atoms specifier  

> delete #8 labels

Expected a keyword  

> close #8.3#8.2

> show #8:CLR

> show #8:CLR,LBN

> view

> ~display HC

> color #8:CLR,LBN cronflowerblue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #8:CLR,LBN cornflowerblue

> color #8:CLR,LBN byhetero

> hide #8 cartoons

> show #!9 models

> select #8:CLR,LBN

416 atoms, 420 bonds, 4 residues, 1 model selected  

> select add #9

416 atoms, 420 bonds, 4 residues, 3 models selected  

> volume zone #9 nearAtoms sel & #8 range 2.5

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2.5

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 4

> volume #9 level 0.02

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2

> select sel : show sel atoms

> ~display HC

> show sel cartoons

> view

> select #7/B:97

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select up

104 atoms, 105 bonds, 7 residues, 1 model selected  

> select up

1725 atoms, 1748 bonds, 114 residues, 1 model selected  

> select up

10144 atoms, 10262 bonds, 640 residues, 1 model selected  

> select down

1725 atoms, 1748 bonds, 114 residues, 1 model selected  

> color sel salmon cartoons

> color sel salmon atoms

> color sel atoms byhet

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color sel byhetero

> hide #!7 models

> show #!7 models

> hide #!7 models

> show #!7 models

> hide #!8 models

> hide #7 atoms

> volume #10 level 0.01096

> hide #!10 models

> show #!8 models

> color #8/B salmon

> color #8/B byhetero

> hide #!7 models

> show #!7 models

> select clear

> surface dust #9 size 4.17

> hide #!9 models

> show #!9 models

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3

> surface dust #9 size 4.17

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.5

> volume #9 level 0.015

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.6

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.8

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.9

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2.5

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 4

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2

> camera ortho

> volume #9 level 0.019

> volume #9 level 0.02

> select #8:LBN

268 atoms, 266 bonds, 2 residues, 1 model selected  

> hide #!9 models

> select #8:703

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> show #!9 models

> select clear

> ui tool show "Side View"

> label #8 protein

Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a
keyword  

> select clear

> volume #9 level 0.025

> volume #9 level 0.0106

> volume #9 level 0.01

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 1.5

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 3

> volume zone #9 nearAtoms #8:CLR,LBN & #8 range 2

> volume #9 level 0.0208

> volume #9 level 0.025

> volume #9 level 0.03

> volume #9 level 0.025

> select #8:LBN,CLR

416 atoms, 420 bonds, 4 residues, 1 model selected  

> select sel : label sel

> label sel text "{0.label_one_letter_code} {0.number}{0.insertion_code}"

> select #8:LBN,CLR

416 atoms, 420 bonds, 4 residues, 1 model selected  

> delete sel label

Expected a keyword  

> delete label sel

Missing or invalid "atoms" argument: invalid atoms specifier  

> ~label sel residues

> select clear

> graphics silhouettes false

> graphics silhouettes true

> select #8/C:703@O3

1 atom, 1 residue, 1 model selected  

> select up

134 atoms, 133 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0
> twoColors true slopColor #ff9300 select true reveal true

0 hydrogen bonds found  
0 strict hydrogen bonds found  

> hide #8.3 models

> show #8.3 models

> save LBN703.tiff supersample 8 transparentBackground true

> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids
> figure/LBN703.cxs" includeMaps true

> save LBN703.tiff supersample 8 transparentBackground true

> select #8:704

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> volume #9 level 0.02

> select clear

> save LBN704.tiff supersample 8 transparentBackground true

> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids
> figure/LBN704.cxs" includeMaps true

> select #8:702

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> volume #9 level 0.015

> volume #9 level 0.01

> volume #9 level 0.02

> show #!10 models

> hide #!9 models

> select add #10

2 models selected  

> surface dust #10 size 4.17

> show #!9 models

> hide #!10 models

> show #!10 models

> hide #!9 models

> select #8:701,702,703,704

499 atoms, 503 bonds, 4 residues, 1 model selected  

> volume zone #10 nearAtoms #8:CLR,LBN & #8 range 2

> volume #10 level 0.01

> volume #10 level 0.011

> volume zone #10 nearAtoms #8:CLR,LBN & #8 range 2.5

> volume zone #10 nearAtoms #8:CLR,LBN & #8 range 3

> volume zone #10 nearAtoms #8:CLR,LBN & #8 range 2

> select clear

> save CLR702.tiff supersample 8 transparentBackground true

> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids
> figure/CLR702.cxs" includeMaps true

> select #8:703

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!10 models

> select clear

> view

> select #8:703

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids
> figure/LBN703.cxs" includeMaps true

> save LBN703.tiff supersample 8 transparentBackground true

> select #8:704

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> save LBN704.tiff supersample 8 transparentBackground true

> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids
> figure/LBN704.cxs" includeMaps true

> select #8:701

157 atoms, 160 bonds, 1 residue, 1 model selected  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> select #8:701

157 atoms, 160 bonds, 1 residue, 1 model selected  

> view sel

No displayed objects specified.  

> select #8:702

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> hide #!9 models

> hide #!10 models

> show #!9 models

> show #!10 models

> select #8:705

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> select #8:701

157 atoms, 160 bonds, 1 residue, 1 model selected  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> view sel

No displayed objects specified.  

> select #8:705

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> save CLR705.tiff supersample 8 transparentBackground true

> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Figure Assembly/Supp Figs/EM lipids
> figure/CLR705.cxs" includeMaps true

> rainbow

> color #7 tan

> undo

> transparency #7 0 cartoons

> color byhetero

> select #8:704

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> select #8:703

134 atoms, 133 bonds, 1 residue, 1 model selected  

> select #8:702

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> select #8:704

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> view

> select #8:704

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> select #8:703

134 atoms, 133 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> color bychain

> select #8:705

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> select clear

> rainbow

> color byhetero

> select #7/B:62

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

> select up

39 atoms, 38 bonds, 3 residues, 1 model selected  

> select up

1725 atoms, 1748 bonds, 114 residues, 1 model selected  

> color sel bychain

> select up

10144 atoms, 10262 bonds, 640 residues, 1 model selected  

> select down

1725 atoms, 1748 bonds, 114 residues, 1 model selected  

> select clear

> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/AtCAT4_ornithine_EM_model/production_from_IFD/pr1000ns_run1_whole_nojump_center_rotxyz-
> transxyz.pdb"

Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/AtCAT4_ornithine_EM_model/production_from_IFD/pr1000ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK GENERATED BY TRJCONV  
  
Ignored bad PDB record found on line 3  
REMARK THIS IS A SIMULATION BOX  
  
pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb title:  
AtCAT4-Orn cryoEM structure in POPC-Cholesterol in water t= 137500.00000 step=
68750000 [more info...]  
  
Chain information for pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb #1  
---  
Chain | Description  
A | No description available  
  
Non-standard residues in pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb
#1  
---  
ACE — (ACE)  
CHL1 — (CHL1)  
CL — (CL)  
NA — (NA)  
NME — (NME)  
ORN — (ORN)  
POPC — (popc)  
SOL — (SOL)  
  

> matchmaker #7 to #8

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 copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb, chain A (#8) with
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb, chain A (#7), sequence alignment
score = 2699.8  
RMSD between 518 pruned atom pairs is 0.000 angstroms; (across all 518 pairs:
0.000)  
  

> hide #!8 models

> show #!8 models

> hide #!7 models

> show #!7 models

> matchmaker #1 to #8

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 copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb, chain A (#8) with
pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb, chain A (#1), sequence
alignment score = 2453.2  
RMSD between 392 pruned atom pairs is 1.068 angstroms; (across all 518 pairs:
2.352)  
  

> hide #!7 models

> hide #!8 models

> hide #8.2 models

> hide #8.3 models

> hide #1 atoms

> protein | #1:CHL1,POPC /A | #1:CHL1,POPC select /A | #1:CHL1,POPC select #1:CHL1,POPC & (/A: show sel atoms

> select #1:CHL1,POPC & (/A: hide sel atoms

> select #1:CHL1,POPC & (/A: hide sel cartoons

> hide sel atoms

> select #1:CHL1,POPC & (/A: show sel atoms

> color sel bychain

> color sel byhetero

> color :CHL1 yellow

> color :CHL1 byhetero

> color :POPC red

> color :POPC byhetero

> ~display HC

> select clear

> view

> show #!8 models

> show #!7 models

> view

> hide #!8 models

> show #!8 models

> hide #!7 models

> hide #!8 models

> view

> show #!7 models

> hide #!7 models

> select #1/A:27

22 atoms, 21 bonds, 1 residue, 1 model selected  

> show sel atoms

> show #!8 models

> hide #!8 models

> show #!7 models

> select #1/C:586@C4

1 atom, 1 residue, 1 model selected  

> select up

74 atoms, 77 bonds, 1 residue, 1 model selected  

> view sel

> hide #1 models

> dssp

> hide #!9 models

> hide #!10 models

> hide #!7 models

> show #!7 models

> close #8.2

> close #8.3

> close #7.2

> show #!8 models

> hide #8 atoms

> select #8/A:250,251,253,257,340,333,178,32

158 atoms, 151 bonds, 8 residues, 1 model selected  

> show sel atoms

> show #8/A:250,251,253,257,340,333,178,32 cartoons

> transparency #7 75 cartoons

> hide #8 cartoons

> show #8/A:250,251,253,257,340,333,178,32 cartoons

> ~display HC

> select #8/A:250,251,253,257,340,333,178,32

158 atoms, 151 bonds, 8 residues, 1 model selected  

> view sel

> combine #8

> show #2:ARG,LYS,HIS,GLU,ASP

> ~display HC

> hide #!2 models

> show #!2 models

> hide #!7 models

> show #!7 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> hide sel atoms

> select up

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel atoms

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> select add #8/A:251@OE2

1 atom, 1 bond, 1 residue, 1 model selected  

> select add #8/A:340@HH22

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

> select add #8/A:32@OD1

3 atoms, 2 bonds, 3 residues, 1 model selected  

> select add #8/A:178@NZ

4 atoms, 2 bonds, 4 residues, 1 model selected  

> select up

8 atoms, 2 bonds, 6 residues, 1 model selected  

> select up

112 atoms, 107 bonds, 6 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #fffb00 interModel false distSlop 0.75 angleSlop 22.0
> twoColors true slopColor #ff9300 select true

18 hydrogen bonds found  
9 strict hydrogen bonds found  

> show sel atoms

> undo

> ui tool show H-Bonds

> select #8/A:250,251,253,257,340,333,178,32

158 atoms, 151 bonds, 6 pseudobonds, 8 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #fffb00 interModel false relax false distSlop 0.75
> angleSlop 22.0 twoColors true slopColor #ff9300 saltOnly true select true

3 hydrogen bonds found  
3 strict hydrogen bonds found  

> ui tool show H-Bonds

> hbonds sel color #fffb00 showDist true interModel false relax false distSlop
> 0.75 angleSlop 22.0 twoColors true slopColor #ff9300 saltOnly true select
> true

3 hydrogen bonds found  
3 strict hydrogen bonds found  

> color #8.2.1 black models

> addh #8:178

Summary of feedback from adding hydrogens to copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8  
---  
notes | No usable SEQRES records for copy of ORN_real_space_refined_063_mapJ510-coot-isolde2_real_space_refined_072-coot.pdb (#8) chain A; guessing termini instead  
No usable SEQRES records for copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb (#8) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A PRO 21, copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/B GLN 1  
Chain-initial residues that are not actual N termini: copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A TYR 456  
Chain-final residues that are actual C termini: copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/B SER 114  
Chain-final residues that are not actual C termini: copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A ALA 583, copy of
ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A GLY 410  
515 hydrogen bonds  
copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A ALA 583 is not terminus, removing
H atom from 'C'  
0 hydrogens added  
  

> ui mousemode right minimize

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 390 (GLY). The set of atoms matches GLY, but the
bonds are different. For more information, see
https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template  
Error with ignoreExternalBonds=True was  
Multiple non-identical matching templates found for residue 80 (CYS): CYM,
CYX.  

> distance #8/A:32@OD2 #8/A:178@HZ1

Distance between copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ1: 2.7Å  

> hide #8.2.1 models

> show #8.2.1 models

> hide #!8.2 models

> show #!8.2 models

> distance #8/A:32@OD2 #8/A:178@HZ3

Distance between copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ3: 2.3Å  

> distance #8/A:32@OD2 #8/A:178@HZ2

Distance between copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ2: 3.3Å  

> hide #3.1 models

> show #3.1 models

> hide #!3 models

> show #!3 models

> close #3

> distance #8/A:32@OD2 #8/A:178@HZ3

Distance between copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb #8/A ASP 32 OD2 and LYS 178 HZ3: 2.3Å  

> color #3 #fffc79ff models

> hide #3.1 models

> show #3.1 models

> color #3.1 black models

> select clear

> color #3 #fffb00ff models

> color #3 black models

> color #8.2 #fff800ff models

> color #3 #fff800ff models

> color #3.1 #008f00ff models

> color #3.1 black models

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

22 atoms, 21 bonds, 1 residue, 1 model selected  

> hide sel atoms

> hide sel cartoons

> select clear

> select #8/A:250,251,257,340,333,178,32

136 atoms, 130 bonds, 4 pseudobonds, 7 residues, 3 models selected  

> select #8/A:250,251,340,333,178,32

112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected  

> select #7/A:257

24 atoms, 23 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select #8/A:257

24 atoms, 23 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel atoms

> hide sel cartoons

> show #!2 models

> hide #!2 models

> hide #7.1 models

> show #7.1 models

> hide #!7 models

> show #!7 models

> show #7 cartoons

> select #8/A:250,251,340,333,178,32

112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected  

> label sel

> label height 0.5

> label height 0.75

> label (#!8 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> select clear

> color #7 cartoon white

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color #7 white cartoons

> color #7 tan cartoons

> color #8.3 #4f8f00ff models

> color #8.3 #009193ff models

> color #8.3 black models

> color #8.2.1 black models

> show #!10 models

> hide #!10 models

> select #8/A:250,251,340,333,178,32

112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected  

> show #!10 models

> volume zone #10 nearAtoms sel & #8 range 2.5

> volume zone #10 nearAtoms sel & #8 range 2

> show #!9 models

Volume zone shortcut requires 1 displayed atomic model and 1 map, got 2 atomic
models, 2 maps.  

> hide #!10 models

> volume zone #9 nearAtoms sel & #8 range 2.5

> volume zone #10 nearAtoms sel & #8 range 2

> show #!10 models

> volume #10 level 0.013

> hide #!9 models

> show #!9 models

> hide #!10 models

> volume #9 level 0.03

> volume zone #10 nearAtoms sel & #8 range 1.9

> volume zone #9 nearAtoms sel & #8 range 1.9

> volume zone #9 nearAtoms sel & #8 range 2

> hide #!9 models

> color #7 grey cartoons

> color #7 lightgrey cartoons

> color #7 white cartoons

> color #7 lightgrey cartoons

> color #7 gainsboro cartoons

> color #7 lightgrey cartoons

> select clear

> select add #7

10144 atoms, 10262 bonds, 1 pseudobond, 640 residues, 2 models selected  

> hide #!7 models

> show #!7 models

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_A SES surface #7.2: minimum, -13.38,
mean 0.08, maximum 16.25  
Coulombic values for ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_B SES surface #7.3: minimum, -11.94,
mean 1.05, maximum 9.69  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide #!7.2 models

> show #7.2 models

> hide #!7.3 models

> show #7.3 models

> hide #!7.3 models

> hide #!7.2 models

> show #7.3 models

> hide #!7.3 models

> show #7.3 models

> hide #!7.3 models

> show #7.3 models

> hide #!7.3 models

> show #7.2 models

> color #7.2 #00000033

> show #7.3 models

> color #7.2 black

> close #7.2-3

> toolshed show

> coulombic sel

Coulombic values for ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_A SES surface #7.2: minimum, -13.38,
mean 0.08, maximum 16.25  
Coulombic values for ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_B SES surface #7.3: minimum, -11.94,
mean 1.05, maximum 9.69  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close #7.2-3

> select #8/A:250,251,340,333,178,32

112 atoms, 107 bonds, 4 pseudobonds, 6 residues, 3 models selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for copy of ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_A SES surface #8.4: minimum, -15.51,
mean 0.01, maximum 16.24  

> close #8.4

> select clear

> select add #7

10144 atoms, 10262 bonds, 1 pseudobond, 640 residues, 2 models selected  

> coulombic sel

Coulombic values for ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_A SES surface #7.2: minimum, -13.38,
mean 0.08, maximum 16.25  
Coulombic values for ORN_real_space_refined_063_mapJ510-coot-
isolde2_real_space_refined_072-coot.pdb_B SES surface #7.3: minimum, -11.94,
mean 1.05, maximum 9.69  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color #7.3 transparent

> color #7.3 black

> color #7.2 transparent

> color #7.2 #00000041

> color #7.2 transparent

> color #7.2 #0000003e

> color #7.2 #0000003d

> close #7.2-3

> select clear

> color #7 grey cartoons

> select clear

> save electrostaticgate.tiff supersample 8 transparentBackground true

> show #!9 models

> show #!10 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> show #!9 models

> show #!10 models

> hide #!10 models

> show #!10 models

> hide #!10 models

> hide #8.2.1 models

> hide #8.3 models

> hide #3.1 models

> hide #!3 models

> hide #!8.2 models

> hide #!8 models

> show #!8 models

> hide #7.1 models

> show #7.1 models

Cell requested for row 4 is out of bounds for table with 13 rows! Resizing
table model.  

> hide #!7 models

> hide #!8 models

> save electrostaticgate_density.tiff supersample 8 transparentBackground true

> show #!7 models

> show #!8 models

> transparency #7 0 cartoons

> show #!8.2 models

> show #8.2.1 models

> show #8.3 models

> hide #!9 models

> show #3.1 models

> hide #!3 models

> show #!3 models

> select #8:orn

22 atoms, 21 bonds, 1 residue, 1 model selected  

> style sel sphere

Changed 22 atom styles  

> show sel atoms


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

Log:
Startup Messages  
---  
warning | Registration file '/Users/ctn700/Library/Application Support/ChimeraX/registration' has expired  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,6
      Model Number: MNWA3DK/A
      Chip: Apple M2 Max
      Total Number of Cores: 12 (8 performance and 4 efficiency)
      Memory: 32 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 6 days, 15 hours, 51 minutes

Graphics/Displays:

    Apple M2 Max:

      Chipset Model: Apple M2 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 38
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        DELL U2720Q:
          Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition)
          UI Looks like: 1920 x 1080 @ 30.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LigandRecognizer: 0.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-locscalesurfer: 0.1.1
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    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: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    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-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-PICKLUSTER: 2.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-TugLigands: 1.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    einops: 0.3.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    fsspec: 2025.5.1
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    mpmath: 1.3.0
    mrcfile: 1.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.24.4
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.10.1
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    sympy: 1.14.0
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    timm: 0.4.12
    tinyarray: 1.2.4
    tomli: 2.0.1
    torch: 2.2.2
    torchvision: 0.17.2
    tornado: 6.4.2
    tqdm: 4.66.6
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 3 months ago

Component: Unassigned → Window Toolkit
Description: modified (diff)
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash on Mac waking from sleep

comment:2 by Eric Pettersen, 3 months ago

Resolution: → duplicate
Status: assigned → closed
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