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Opened 4 months ago
Last modified 4 months ago
#18310 closed defect
ChimeraX bug report submission — at Initial Version
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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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{
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===== Log before crash start =====
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: 1.8 (2024-06-10)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 5J4I
Summary of feedback from opening 5J4I fetched from pdb
---
note | Fetching compressed mmCIF 5j4i from http://files.rcsb.org/download/5j4i.cif
5j4i title:
Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2
Angstroem resolution [more info...]
Chain information for 5j4i #1
---
Chain | Description | UniProt
A B | Arginine/agmatine antiporter | ADIC_ECO57 1-445
> open 8kdp
Summary of feedback from opening 8kdp fetched from pdb
---
note | Fetching compressed mmCIF 8kdp from http://files.rcsb.org/download/8kdp.cif
8kdp title:
Structure of apo outward-open LAT1-CD98h in nanodisc, focused on TMD [more
info...]
Chain information for 8kdp #2
---
Chain | Description | UniProt
A | 4F2 cell-surface antigen heavy chain | 4F2_HUMAN 2-630
B | Large neutral amino acids transporter small subunit 1 | LAT1_HUMAN 1-507
> hide #1 models
> show #!2 atoms
> dssp
> hide #!2 atoms
> open 7O82
Summary of feedback from opening 7O82 fetched from pdb
---
note | Fetching compressed mmCIF 7o82 from http://files.rcsb.org/download/7o82.cif
7o82 title:
The L-arginine/agmatine antiporter from E. coli at 1.7 A resolution [more
info...]
Chain information for 7o82 #3
---
Chain | Description | UniProt
A B | Arginine/agmatine antiporter | ADIC_ECO57 1-445
Non-standard residues in 7o82 #3
---
BNG — nonyl beta-D-glucopyranoside (Beta-NONYLGLUCOSIDE; nonyl beta-D-
glucoside; nonyl D-glucoside; nonyl glucoside)
D10 — decane
HEX — hexane
OCT — N-octane
TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer)
78 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
> hide #!2 models
> view
> dssp
> show #3:HOH
> select #3/A:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #3/A:22
14 atoms, 12 bonds, 2 residues, 1 model selected
> view sel
> select clear
> show #3 atoms
> rainbow #3
> color #3 byhetero
> show #!2 models
> matchmaker #3 to #2
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 8kdp, chain B (#2) with 7o82, chain B (#3), sequence alignment
score = 634
RMSD between 190 pruned atom pairs is 1.228 angstroms; (across all 407 pairs:
5.717)
> view
> dssp
> hide #3#!2 cartoons
> show #3#!2 cartoons
> hide #3#!2 atoms
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
> step7_3_whole_nojump_center_rotxyz-transxyz.pdb"
Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
step7_3_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
nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb title:
AtCAT4-Leu in POPC-Cholesterol in water t= 1000000.00000 step= 500000000 [more
info...]
Chain information for nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb
#4
---
Chain | Description
A | No description available
Non-standard residues in nowaters-step7_3_whole_nojump_center_rotxyz-
transxyz.pdb #4
---
ACE — (ACE)
CHL1 — (CHL1)
NME — (NME)
POPC — (popc)
> hide #3 models
> hide #!2 models
> view
> hide :POPC,CHL1
> dssp
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
> step7_2_whole_nojump_center_rotxyz-transxyz.pdb"
Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/AtCAT4_MD_model_to_test_TM1/pr1000ns/nowaters-
step7_2_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
nowaters-step7_2_whole_nojump_center_rotxyz-transxyz.pdb title:
AtCAT4-Leu in POPC-Cholesterol in water t= 1000000.00000 step= 500000000 [more
info...]
Chain information for nowaters-step7_2_whole_nojump_center_rotxyz-transxyz.pdb
#5
---
Chain | Description
A | No description available
Non-standard residues in nowaters-step7_2_whole_nojump_center_rotxyz-
transxyz.pdb #5
---
ACE — (ACE)
CHL1 — (CHL1)
NME — (NME)
POPC — (popc)
> hide #4 models
> hide :POPC,CHL1
> dssp
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead Lab/Postdoc/MD/AtCAT4_new_model_to_test_TM1/pr1000ns/nowaters-
> step7_3_whole_nojump_center_rotxyz-transxyz.pdb"
Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/Dimitris - Newstead
Lab/Postdoc/MD/AtCAT4_new_model_to_test_TM1/pr1000ns/nowaters-
step7_3_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
nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb title:
AtCAT4 cryoEM structure in POPC-Cholesterol in water t= 1000000.00000 step=
500000000 [more info...]
Chain information for nowaters-step7_3_whole_nojump_center_rotxyz-transxyz.pdb
#6
---
Chain | Description
A | No description available
Non-standard residues in nowaters-step7_3_whole_nojump_center_rotxyz-
transxyz.pdb #6
---
ACE — (ACE)
CHL1 — (CHL1)
NME — (NME)
POPC — (popc)
> hide #5 models
> hide :POPC,CHL1
> close #1,3-6#2
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/SLC7A4_homology_model_leucine/SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb"
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
title:
Alphafold monomer V2.0 prediction for cationic amino acid transporter 4
(O43246) [more info...]
Chain information for
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1
---
Chain | Description
A | No description available
Non-standard residues in
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1
---
CLR — (CLR)
> dssp
> 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 #2
---
Chain | Description
A | No description available
Non-standard residues in pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb
#2
---
ACE — (ACE)
CHL1 — (CHL1)
CL — (CL)
NA — (NA)
NME — (NME)
ORN — (ORN)
POPC — (popc)
SOL — (SOL)
> matchmaker #2 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb, chain
A (#2), sequence alignment score = 1246.3
RMSD between 357 pruned atom pairs is 1.098 angstroms; (across all 547 pairs:
7.014)
> hide atoms
> view
> dssp
> hide #!1 models
> hide #2 models
> open /Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Apo_Sybody/RealSpaceRefine_34/AtCAT4_final-
> coot-17_H_real_space_refined_034_ARG-fixed_H.pdb
Chain information for AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
fixed_H.pdb #3
---
Chain | Description
A | No description available
B | No description available
> view
> dssp
> undo
> dssp
> undo
> dssp
> ui tool show "Modeller Comparative"
Populating font family aliases took 61 ms. Replace uses of missing font family
"Times" with one that exists to avoid this cost.
> ui tool show "Modeller Comparative"
> ui tool show "Show Sequence Viewer"
> open /Users/ctn700/Downloads/AF-O43246-F1-model_v4.pdb
AF-O43246-F1-model_v4.pdb title:
Alphafold monomer V2.0 prediction for cationic amino acid transporter 4
(O43246) [more info...]
Chain information for AF-O43246-F1-model_v4.pdb #4
---
Chain | Description | UniProt
A | cationic amino acid transporter 4 | CTR4_HUMAN 1-635
> matchmaker #4 to #3
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 1197.6
RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
5.348)
> view
> ui tool show "Show Sequence Viewer"
> sequence chain #3/A
Alignment identifier is 3/A
> sequence chain #4/A
Alignment identifier is 4/A
> select add #3
9769 atoms, 9888 bonds, 1 pseudobond, 634 residues, 2 models selected
> select add #4
14590 atoms, 14841 bonds, 1 pseudobond, 1269 residues, 3 models selected
> select clear
> select #3/A,#4
Expected an objects specifier or a keyword
> select #3/A#4
12861 atoms, 13090 bonds, 1 pseudobond, 1154 residues, 3 models selected
> ui tool show "Modeller Comparative"
Alignment identifier is 3/A
Alignment identifier is 4/A
> ui tool show Matchmaker
> matchmaker #4 to #3
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 1197.6
RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
5.348)
> ui tool show Matchmaker
> matchmaker #4 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 2556.8
RMSD between 251 pruned atom pairs is 1.141 angstroms; (across all 556 pairs:
9.086)
> ui tool show Matchmaker
> matchmaker #4 to #3
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 1197.6
RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
5.348)
> ui tool show "Modeller Comparative"
> ui tool show "Blast Protein"
> ui tool show Matchmaker
> matchmaker #4 to #3/A pairing bs
Parameters
---
Chain pairing | bs
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 1197.6
RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
5.348)
> matchmaker #4 to #3/A pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 1197.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
5.348)
> matchmaker #4 to #3/A pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment
score = 1197.6
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 283 pruned atom pairs is 1.159 angstroms; (across all 505 pairs:
5.348)
> ui tool show "Modeller Comparative"
> modeller comparative 1:2 numModels 5 fast false multichain false hetPreserve
> true hydrogens true waterPreserve true
Webservices job id: 63RUMTGUXZHWP15D
Modeller job (ID 63RUMTGUXZHWP15D) finished
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 531.6
RMSD between 8 pruned atom pairs is 1.367 angstroms; (across all 501 pairs:
22.621)
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 404.2
RMSD between 8 pruned atom pairs is 1.235 angstroms; (across all 501 pairs:
32.296)
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 452.9
RMSD between 5 pruned atom pairs is 0.956 angstroms; (across all 494 pairs:
21.034)
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 472.8
RMSD between 10 pruned atom pairs is 1.324 angstroms; (across all 492 pairs:
23.779)
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 449.9
RMSD between 7 pruned atom pairs is 0.902 angstroms; (across all 494 pairs:
24.766)
Associated chain_A chain A to AF-O43246-F1-model_v4.pdb, chain A with 0
mismatches
Chain information for chain_A
---
Chain | Description
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A | No description available
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A, chain_A #5.1/A, chain_A #5.2/A, chain_A
#5.3/A, chain_A #5.4/A, chain_A #5.5/A
> hide #4 models
> matchmaker #5 to #3
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#5.1), sequence alignment score = 531.6
RMSD between 8 pruned atom pairs is 1.367 angstroms; (across all 501 pairs:
22.621)
Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#5.2), sequence alignment score = 404.2
RMSD between 8 pruned atom pairs is 1.235 angstroms; (across all 501 pairs:
32.296)
Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#5.3), sequence alignment score = 452.9
RMSD between 5 pruned atom pairs is 0.956 angstroms; (across all 494 pairs:
21.034)
Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#5.4), sequence alignment score = 472.8
RMSD between 10 pruned atom pairs is 1.324 angstroms; (across all 492 pairs:
23.779)
Matchmaker AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#5.5), sequence alignment score = 449.9
RMSD between 7 pruned atom pairs is 0.902 angstroms; (across all 494 pairs:
24.766)
> hide #!3 models
> hide #5.2 models
> hide #5.3 models
> hide #5.4 models
> hide #5.5 models
> hide #5.1 models
> show #5.2 models
> hide #5.2 models
> show #5.3 models
> hide #5.3 models
> show #5.4 models
> hide #5.4 models
> show #5.5 models
> hide #5.5 models
> close #5
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A
> ui tool show "Modeller Comparative"
> modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens true waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: 4HXLBUSRUEWDV4Z9
Modeller job (ID 4HXLBUSRUEWDV4Z9) finished
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 377.6
RMSD between 11 pruned atom pairs is 1.363 angstroms; (across all 494 pairs:
19.118)
Associated chain_A chain A to AF-O43246-F1-model_v4.pdb, chain A with 0
mismatches
Chain information for chain_A
---
Chain | Description
5.1/A | No description available
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A, chain_A #5.1/A
> close #5
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A
> ui tool show "Modeller Comparative"
> modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve false directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: SQ53K70VGRRVFOCB
Modeller job (ID SQ53K70VGRRVFOCB) finished
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with chain_A, chain A (#), sequence alignment score = 533.4
RMSD between 9 pruned atom pairs is 1.333 angstroms; (across all 494 pairs:
16.579)
Associated chain_A chain A to AF-O43246-F1-model_v4.pdb, chain A with 0
mismatches
Chain information for chain_A
---
Chain | Description
5.1/A | No description available
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A, chain_A #5.1/A
> show #!3 models
> hide #!3 models
> close #5
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AF-O43246-F1-model_v4.pdb #4/A
> open "/Users/ctn700/Library/CloudStorage/OneDrive-Nexus365/Dimitris -
> Newstead
> Lab/Postdoc/MD/AtCAT4_new_model_to_test_TM1/setup_new/system_solvated_ions.gro"
Chain information for AtCAT4 cryoEM structure in POPC-Cholesterol in water #5
---
Chain | Description
? | No description available
> hide #5:POPC,CHL1,SOL
> view
> matchmaker #5 to #3
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain
(blank) (#5), sequence alignment score = 2528.4
RMSD between 504 pruned atom pairs is 0.372 angstroms; (across all 517 pairs:
0.601)
> show #!3 models
> view
> hide #!3 models
> select add #3
14590 atoms, 14841 bonds, 1 pseudobond, 1269 residues, 3 models selected
> select subtract #3
4821 atoms, 4953 bonds, 635 residues, 1 model selected
> select #5,4
162643 atoms, 128423 bonds, 35494 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #4 to #5/? pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment score =
1209.8
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AF-O43246-F1-model_v4.pdb
#4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 285 pruned atom pairs is 1.152 angstroms; (across all 545 pairs:
8.655)
> show #4 models
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens true waterPreserve false directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: I9KJIO2YLDJMCQO1
Modeller job (ID I9KJIO2YLDJMCQO1) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 76, in
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
4.18.0-553.62.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/07/27 11:39:01
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
allhmodel__W> The class 'allhmodel' is deprecated; use 'AllHModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 283002 276.369
0.270
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 298535 291.538
0.285
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 314385 307.017
0.300
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 346085 337.974
0.330
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 409485 399.888
0.391
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 536285 523.716
0.511
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 538537 525.915 0.514
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 541073 528.392 0.516
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 543609 530.868 0.518
read_al_374_> Non-standard residue type,position,sequence: . 1 1
read_al_374_> Non-standard residue type,position,sequence: . 564 1
Read the alignment from file : alignment.ali
Total number of alignment positions: 652
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 AtCAT4_cr 564 1 AtCAT4_cryo
2 AF-O43246 635 1 AF-O43246-F
3 chain_A 635 1 chain_A
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./AtCAT4_cryoEM_structure_in_POPC-
Cholesterol_in_water_5.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 714534 697.787
0.681
read_pd_459W> Residue type ACE not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 714534 697.787 0.681
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 714705 697.954
0.682
read_pd_459W> Residue type HID not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 715555 698.784
0.682
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 716813 700.013
0.684
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 718717 701.872
0.685
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 721573 704.661
0.688
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 725857 708.845
0.692
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 725857 708.845 0.692
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 725947 708.933
0.692
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 732373 715.208
0.698
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 732373 715.208 0.698
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 732508 715.340
0.699
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 742130 724.736
0.708
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 742130 724.736 0.708
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 742328 724.930
0.708
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 756778 739.041
0.722
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 756778 739.041 0.722
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 757075 739.331
0.722
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 778733 760.481
0.743
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 778733 760.481 0.743
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779183 760.921
0.743
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 811687 792.663
0.774
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 811687 792.663 0.774
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 812362 793.322
0.775
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 861118 840.936
0.821
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 861118 840.936 0.821
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 862126 841.920
0.822
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 935260 913.340
0.892
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 935260 913.340 0.892
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 936772 914.816
0.893
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1046456 1021.930
0.998
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1046456 1021.930
0.998
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1048724 1024.145
1.000
rdpdb___459W> Residue type NME not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1046987 1022.448
0.998
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 3)
Alignment .PHQLAKKLSAVDLVAIGVGTTIGAGVYILVGTVAREHTGPALAVSFFIAGVAAALS
PDB .P.QLAKKLSAVDLVAIGVGTTIGAGVYILVGTVARE.TGPALAVSFFIAGVAAALS
Match ** ********************************** *******************
Alignment residue type 7 (H, HIS) does not match pdb
residue type 68 (., HID),
for align code AtCAT4_cryoEM_structure_in_POPC-Choleste (atom file
AtCAT4_cryoEM_structure_in_POPC-Cholesterol_in_water_5), pdb residue number "
22", chain ""
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 AtCAT4_cryoEM_structure_in_POPC-Choleste
No output models from Modeller; see log for Modeller text output.
> hide #4 models
> select subtract #4
157822 atoms, 123470 bonds, 34859 residues, 1 model selected
> select #5:HID
102 atoms, 102 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel sphere
Changed 102 atom styles
> style sel ball
Changed 102 atom styles
> hide #5 atoms
> select #5:HID
102 atoms, 102 bonds, 6 residues, 1 model selected
> show sel atoms
> style sel ball
Changed 102 atom styles
> ui mousemode right swapaa
> swappa
Unknown command: swappa
> swapaa
Missing or invalid "residues" argument: empty atom specifier
> help swapaa
> swapaa #5:HID
Missing or invalid "resTypes" argument: Expected a text string
> swapaa #5:HID HIS
Using Dunbrack library
AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 22: phi -77.6,
psi 67.8 trans
AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 57: phi -136.9,
psi 159.9 trans
AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 95: phi -58.0,
psi -46.7 trans
AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 520: phi -53.6,
psi 134.2 trans
AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 524: phi -157.4,
psi -172.6 trans
AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? HID 577: phi -103.8,
psi 7.8 trans
Applying HIS rotamer (chi angles: -64.5 -70.6) to AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? HIS 22
Applying HIS rotamer (chi angles: -62.6 -79.6) to AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? HIS 57
Applying HIS rotamer (chi angles: -179.8 72.7) to AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? HIS 95
Applying HIS rotamer (chi angles: -173.8 -75.5) to AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? HIS 520
Applying HIS rotamer (chi angles: 61.8 81.6) to AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? HIS 524
Applying HIS rotamer (chi angles: -173.8 -172.5) to AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? HIS 577
> delete #5:POPC,CHL1,SOL
> select add #5
8746 atoms, 8530 bonds, 869 residues, 1 model selected
> show sel atoms
> undo
> delete #5:POPC,CHL1,SOL,CL,NA
> show sel atoms
> undo
> addh #5:HIS
Summary of feedback from adding hydrogens to AtCAT4 cryoEM structure in POPC-
Cholesterol in water #5
---
warnings | Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/? PRO 152 CG because it is missing heavy-atom bond partners
Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
#5/? PRO 152 CB because it is missing heavy-atom bond partners
Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
#5/? LEU 476 CG because it is missing heavy-atom bond partners
Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
#5/? LEU 476 HG because it is missing heavy-atom bond partners
Not adding hydrogens to AtCAT4 cryoEM structure in POPC-Cholesterol in water
#5/? LEU 476 CD1 because it is missing heavy-atom bond partners
1 messages similar to the above omitted
notes | No usable SEQRES records for AtCAT4 cryoEM structure in POPC-Cholesterol in water (#5) chain (blank); guessing termini instead
Chain-initial residues that are actual N termini: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? ACE 20
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/? NME 583
Chain-final residues that are not actual C termini:
462 hydrogen bonds
33 hydrogens added
> select clear
> show #4 models
> hide #4 models
> select add #4
4821 atoms, 4953 bonds, 635 residues, 1 model selected
> select add #5
13295 atoms, 13516 bonds, 1199 residues, 2 models selected
> ui tool show Matchmaker
> matchmaker #4 to #5/? pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment score =
1209.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AF-O43246-F1-model_v4.pdb
#4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 285 pruned atom pairs is 1.152 angstroms; (across all 545 pairs:
8.655)
> ui tool show "Modeller Comparative"
> modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens true waterPreserve false directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: 03PC2J0R944H8KUG
Modeller job (ID 03PC2J0R944H8KUG) finished
Parameters
---
Chain pairing | ss
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with chain_A, chain (blank) (#), sequence alignment score = 284.4
RMSD between 12 pruned atom pairs is 1.489 angstroms; (across all 530 pairs:
29.745)
Associated chain_A chain to AF-O43246-F1-model_v4.pdb, chain A with 0
mismatches
Chain information for chain_A
---
Chain | Description
6.1/? | No description available
Chains used in RMSD evaluation for alignment 1: AF-O43246-F1-model_v4.pdb
#4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?, chain_A
#6.1/?
> hide #5 models
> close #6
Chains used in RMSD evaluation for alignment 1: AF-O43246-F1-model_v4.pdb
#4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?
> show #4 models
> show #5 models
> select clear
> delete #4:1-30
> delete #4:594-600
> delete #4:594-636
> ui tool show Matchmaker
> matchmaker #!4 to #5/? pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with AF-O43246-F1-model_v4.pdb, chain A (#4), sequence alignment score =
1214.1
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AF-O43246-F1-model_v4.pdb
#4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 286 pruned atom pairs is 1.148 angstroms; (across all 543 pairs:
8.534)
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens true waterPreserve false directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: 12UKJZ1RC6WQUGV9
Modeller job (ID 12UKJZ1RC6WQUGV9) finished
Parameters
---
Chain pairing | ss
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with chain_A, chain (blank) (#), sequence alignment score = 268
RMSD between 6 pruned atom pairs is 1.324 angstroms; (across all 537 pairs:
25.813)
Associated chain_A chain to AF-O43246-F1-model_v4.pdb, chain A with 0
mismatches
Chain information for chain_A
---
Chain | Description
6.1/? | No description available
Chains used in RMSD evaluation for alignment 2: AF-O43246-F1-model_v4.pdb
#4/A, AtCAT4 cryoEM structure in POPC-Cholesterol in water #5/?, chain_A
#6.1/?
> hide #5 models
> hide #!4 models
> show #5 models
> show #!4 models
> show #!1 models
> hide #!4 models
> hide #!6 models
> hide #6.1 models
> hide #5 models
> show #!4 models
> show #2 models
> hide #2 models
> hide #!4 models
> view
> select add #1
8573 atoms, 8694 bonds, 1 pseudobond, 558 residues, 2 models selected
> show sel atoms
> select subtract #1
Nothing selected
> open uniprot:O43246
Summary of feedback from opening O43246 fetched from uniprot
---
notes | Fetching compressed O43246 UniProt info from https://www.uniprot.org/uniprot/O43246.xml
Alignment identifier is O43246
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to O43246 with 0 mismatches
Associated AF-O43246-F1-model_v4.pdb chain A to O43246 with 0 mismatches
Associated chain_A (6.1) chain to O43246 with 0 mismatches
Opened UniProt O43246
> select #1/A:38-592 #4/A #6.1/*
22461 atoms, 22833 bonds, 1753 residues, 3 models selected
> hide #!1 models
> view
> select #1/A:151,195,221,500 #4/A:151,195,221,500 #6.1/*:151,195,221,500,601
158 atoms, 145 bonds, 13 residues, 3 models selected
> select #1/A:422,427 #4/A:422,427 #6.1/*:422,427
56 atoms, 50 bonds, 6 residues, 3 models selected
> select #1/A:155-192 #4/A:155-192 #6.1/*:155-192
1388 atoms, 1412 bonds, 114 residues, 3 models selected
> select #6.1/*:28,349,608 #1/A:349 #4/A:349
59 atoms, 55 bonds, 5 residues, 3 models selected
> select
> #1/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
> #4/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
> #6.1/*:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
10371 atoms, 10473 bonds, 819 residues, 3 models selected
> select #1/A:422,427 #4/A:422,427 #6.1/*:422,427
56 atoms, 50 bonds, 6 residues, 3 models selected
> select #1/A:38-592 #4/A #6.1/*
22461 atoms, 22833 bonds, 1753 residues, 3 models selected
> select #1/A:38-592 #4/A #6.1/*
22461 atoms, 22833 bonds, 1753 residues, 3 models selected
> ~select
Nothing selected
> select #1/A:151,195,221,500 #4/A:151,195,221,500 #6.1/*:151,195,221,500,601
158 atoms, 145 bonds, 13 residues, 3 models selected
> select #1/A:422,427 #4/A:422,427 #6.1/*:422,427
56 atoms, 50 bonds, 6 residues, 3 models selected
> select #1/A:155-192 #4/A:155-192 #6.1/*:155-192
1388 atoms, 1412 bonds, 114 residues, 3 models selected
> select #1/A:155-192 #4/A:155-192 #6.1/*:155-192
1388 atoms, 1412 bonds, 114 residues, 3 models selected
> ~select
Nothing selected
> select #6.1/*:28,349,608 #1/A:349 #4/A:349
59 atoms, 55 bonds, 5 residues, 3 models selected
> select #1/A:349 #4/A:349 #6.1/*:349
25 atoms, 22 bonds, 3 residues, 3 models selected
> select
> #1/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
> #4/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
> #6.1/*:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
10371 atoms, 10473 bonds, 819 residues, 3 models selected
> select
> #1/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
> #4/A:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
> #6.1/*:42-62,66-86,113-133,197-217,229-249,270-290,318-338,365-385,391-411,478-498,508-528,539-559,567-587
10371 atoms, 10473 bonds, 819 residues, 3 models selected
> open /Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Apo_Sybody/RealSpaceRefine_34/AtCAT4_final-
> coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
Chain information for AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
fixed_noH.pdb #7
---
Chain | Description
A | No description available
B | No description available
> view
> select add #6.1
15910 atoms, 16110 bonds, 1181 residues, 3 models selected
> select add #6
15910 atoms, 16110 bonds, 1181 residues, 4 models selected
> select subtract #6
6188 atoms, 6256 bonds, 546 residues, 2 models selected
> select add #4
8448 atoms, 8602 bonds, 836 residues, 2 models selected
> select subtract #4
4183 atoms, 4217 bonds, 273 residues, 1 model selected
> select add #1
8573 atoms, 8694 bonds, 1 pseudobond, 558 residues, 2 models selected
> select subtract #1
Nothing selected
> select add #6.1
9722 atoms, 9854 bonds, 635 residues, 1 model selected
> select add #7
14540 atoms, 14789 bonds, 1 pseudobond, 1269 residues, 3 models selected
> ui tool show "Show Sequence Viewer"
> sequence chain #5/?
Alignment identifier is 5/
> ui tool show "Modeller Comparative"
> select #5/*:20
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/*
8474 atoms, 8563 bonds, 564 residues, 1 model selected
> modeller comparative "5/ :1" numModels 5 fast true multichain false
> hetPreserve false hydrogens true waterPreserve false directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: TBAIP49CM3LNEJ9G
Modeller job (ID TBAIP49CM3LNEJ9G) finished
Parameters
---
Chain pairing | ss
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with chain_(blank), chain (blank) (#), sequence alignment score = 2835.8
RMSD between 562 pruned atom pairs is 0.171 angstroms; (across all 562 pairs:
0.171)
Associated chain_(blank) chain to chain (blank) with 0 mismatches
Chain information for chain_(blank)
---
Chain | Description
8.1/? | No description available
> hide #!7 models
> select #8.1/?:25
10 atoms, 9 bonds, 1 residue, 1 model selected
> select up
294 atoms, 294 bonds, 21 residues, 1 model selected
> show sel atoms
> close #8
> ui tool show "Modeller Comparative"
> ui tool show Matchmaker
> matchmaker #!7 to #6.1/? pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 chain_A, chain (blank) (#6.1) with AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain A (#7), sequence
alignment score = 192.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 9 pruned atom pairs is 1.656 angstroms; (across all 492 pairs:
25.311)
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: W5UOTIFQA72M2SV2
Modeller job (ID W5UOTIFQA72M2SV2) finished
Parameters
---
Chain pairing | ss
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 chain_A, chain (blank) (#6.1) with chain_(blank), chain (blank)
(#), sequence alignment score = 2716.2
RMSD between 29 pruned atom pairs is 1.279 angstroms; (across all 635 pairs:
30.341)
Associated chain_(blank) chain to chain_A, chain (blank) with 0 mismatches
Chain information for chain_(blank)
---
Chain | Description
8.1/? | No description available
Associated chain_(blank) (8.1) chain to O43246 with 0 mismatches
Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A, chain_(blank) #8.1/?
> close #8
Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Alignment identifier is 1/A
Alignment identifier is 2/A
Alignment identifier is 2
Alignment identifier is 3
Missing or invalid "chains" argument: only initial part "#4/A#6.1" of atom
specifier valid
> show #5 models
> matchmaker #5 to #6.1/? pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 chain_A, chain (blank) (#6.1) with AtCAT4 cryoEM structure in POPC-
Cholesterol in water, chain (blank) (#5), sequence alignment score = 268
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?, chain_A #6.1/?
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 6 pruned atom pairs is 1.324 angstroms; (across all 537 pairs:
25.813)
> ui tool show "Modeller Comparative"
> modeller comparative 2:1 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Webservices job id: SEB9H6EJPN7GVBAZ
Modeller job (ID SEB9H6EJPN7GVBAZ) finished
Parameters
---
Chain pairing | ss
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 chain_A, chain (blank) (#6.1) with chain_(blank), chain (blank)
(#), sequence alignment score = 2749.8
RMSD between 90 pruned atom pairs is 1.442 angstroms; (across all 635 pairs:
28.278)
Associated chain_(blank) chain to chain_A, chain (blank) with 0 mismatches
Chain information for chain_(blank)
---
Chain | Description
8.1/? | No description available
Associated chain_(blank) (8.1) chain to O43246 with 0 mismatches
Associated chain_(blank) (8.1) chain to chain_A, chain (blank) with 0
mismatches
Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A, chain_(blank) #8.1/?
Chains used in RMSD evaluation for alignment 2: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?, chain_A #6.1/?, chain_(blank) #8.1/?
> close #8
Chains used in RMSD evaluation for alignment 2: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?, chain_A #6.1/?
Chains used in RMSD evaluation for alignment 1: chain_A #6.1/?, AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> open /Users/ctn700/Downloads/9fqw.cif
9fqw.cif title:
Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the ornithine-bound
inward-occluded state [more info...]
Chain information for 9fqw.cif #8
---
Chain | Description | UniProt
A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871
B | Surface protein | ENV_MLVF5 35-270
Non-standard residues in 9fqw.cif #8
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
ORN — L-ornithine
Y01 — cholesterol hemisuccinate
> hide #5 models
> dssp #8
> set bgColor white
> lighting soft
> view
> undo
> select #8/A:1003@OXT
1 atom, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> view sel
> open /Users/ctn700/Downloads/emd_50671.map
Opened emd_50671.map as #9, grid size 256,256,256, pixel 0.825, shown at level
0.0937, step 1, values float32
> transparency 50
> volume #9 level 0.1513
> view
> surface dust #9 size 8.25
> open 9fqu
Summary of feedback from opening 9fqu fetched from pdb
---
note | Fetching compressed mmCIF 9fqu from http://files.rcsb.org/download/9fqu.cif
9fqu title:
Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the arginine-bound inward-
occluded state [more info...]
Chain information for 9fqu #10
---
Chain | Description | UniProt
A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871
B | Surface protein | ENV_MLVF5 35-270
Non-standard residues in 9fqu #10
---
ARG — arginine
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Y01 — cholesterol hemisuccinate
> matchmaker #10 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 9fqw.cif, chain A (#8) with 9fqu, chain A (#10), sequence alignment
score = 4093.9
RMSD between 543 pruned atom pairs is 0.305 angstroms; (across all 544 pairs:
0.317)
> hide #!9 models
> camera mono
> view sel
> select #10/A:263
12 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!8 models
> matchmaker #10 to #7
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with 9fqu, chain A (#10), sequence alignment score = 1155.9
RMSD between 156 pruned atom pairs is 1.204 angstroms; (across all 494 pairs:
6.473)
> show #!7 models
> matchmaker #10 to #3
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_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb,
chain A (#3) with 9fqu, chain A (#10), sequence alignment score = 1127.7
RMSD between 157 pruned atom pairs is 1.208 angstroms; (across all 494 pairs:
6.467)
> show #!3 models
> hide #!7 models
> hide #!3 models
> show #!3 models
> hide #!3 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 #11
---
Chain | Description
A | No description available
B | 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 9fqu, chain A (#10) with ORN_real_space_refined_063_mapJ510-coot-
sn.pdb, chain A (#11), sequence alignment score = 1139.9
RMSD between 142 pruned atom pairs is 1.235 angstroms; (across all 491 pairs:
6.291)
> hide #!10 models
> show #!8 models
> matchmaker #8 to #11
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 ORN_real_space_refined_063_mapJ510-coot-sn.pdb, chain A (#11) with
9fqw.cif, chain A (#8), sequence alignment score = 1167.5
RMSD between 140 pruned atom pairs is 1.231 angstroms; (across all 491 pairs:
6.347)
> show #!9 models
> hide #!9 models
> view
> hide #!11 models
> view
> open 9FQT
Summary of feedback from opening 9FQT fetched from pdb
---
note | Fetching compressed mmCIF 9fqt from http://files.rcsb.org/download/9fqt.cif
9fqt title:
Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inward-open state
[more info...]
Chain information for 9fqt #12
---
Chain | Description | UniProt
A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871
B | Surface protein | ENV_MLVF5 1-236
Non-standard residues in 9fqt #12
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Y01 — cholesterol hemisuccinate
> matchmaker #12 to #11
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 ORN_real_space_refined_063_mapJ510-coot-sn.pdb, chain A (#11) with
9fqt, chain A (#12), sequence alignment score = 1179.2
RMSD between 121 pruned atom pairs is 1.230 angstroms; (across all 487 pairs:
7.631)
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
17 atoms, 16 bonds, 1 residue, 1 model selected
> view sel
> show #!7 models
> show #!10 models
> hide #!7 models
> hide #!8 models
> close #8-12
> show #!7 models
> view
> open 9FQT
9fqt title:
Cryo-EM structure of MmCAT1 bound with FrMLV-RBD in the apo inward-open state
[more info...]
Chain information for 9fqt #8
---
Chain | Description | UniProt
A | High affinity cationic amino acid transporter 1,Green fluorescent protein | CTR1_MOUSE 13-622, GFP_AEQVI 635-871
B | Surface protein | ENV_MLVF5 1-236
Non-standard residues in 9fqt #8
---
BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose)
FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose;
L-fucose; fucose)
MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose)
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)
Y01 — cholesterol hemisuccinate
> matchmaker #8 to #7
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with 9fqt, chain A (#8), sequence alignment score = 1188.6
RMSD between 121 pruned atom pairs is 1.131 angstroms; (across all 490 pairs:
7.971)
> matchmaker #8 to #7:87-224,282-405,465-579
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with 9fqt, chain A (#8), sequence alignment score = 787.4
RMSD between 103 pruned atom pairs is 1.145 angstroms; (across all 349 pairs:
12.749)
> view
> dssp
> lighting soft
> ui tool show Matchmaker
> matchmaker #!7 to #8/A pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 9fqt, chain A (#8) with AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain A (#7), sequence
alignment score = 1188.6
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A, 9fqt #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 121 pruned atom pairs is 1.131 angstroms; (across all 490 pairs:
7.971)
> select #7:87-224,282-405,465-579
3022 atoms, 3096 bonds, 405 residues, 1 model selected
> select #8/A:91
16 atoms, 15 bonds, 1 residue, 1 model selected
> select #8/A:91-92
30 atoms, 30 bonds, 2 residues, 1 model selected
> select #7:87-224,282-405,465-579
3022 atoms, 3096 bonds, 405 residues, 1 model selected
The cached device pixel ratio value was stale on window expose. Please file a
QTBUG which explains how to reproduce.
> matchmaker #8/A:91-244,302-425,498-602 to #7/A:87-224,282-405,465-579
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with 9fqt, chain A (#8), sequence alignment score = 781.8
RMSD between 104 pruned atom pairs is 1.155 angstroms; (across all 359 pairs:
8.462)
> ui tool show Matchmaker
> matchmaker #!8 to #6.1/? pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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 chain_A, chain (blank) (#6.1) with 9fqt, chain A (#8), sequence
alignment score = 409.2
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: chain_A #6.1/?, 9fqt #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 7 pruned atom pairs is 1.033 angstroms; (across all 513 pairs:
22.270)
> show #!6 models
> undo
> hide #!7 models
> show #!6 models
> show #6.1 models
> hide #!8 models
> close #6.1
> close #6
> open uniprot:O43246
Summary of feedback from opening O43246 fetched from uniprot
---
notes | Alignment identifier is O43246
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to O43246 with 0 mismatches
Associated AF-O43246-F1-model_v4.pdb chain A to O43246 with 0 mismatches
Opened UniProt O43246
> ui tool show Matchmaker
> open uniprot:O43246
Summary of feedback from opening O43246 fetched from uniprot
---
notes | Alignment identifier is O43246
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to O43246 with 0 mismatches
Associated AF-O43246-F1-model_v4.pdb chain A to O43246 with 0 mismatches
Opened UniProt O43246
> select #1/A:38-592 #4/A
12739 atoms, 12979 bonds, 1118 residues, 2 models selected
> select #1/A:38-592 #4/A
12739 atoms, 12979 bonds, 1118 residues, 2 models selected
> ~select
Nothing selected
> select #1/A:151,195,221,500 #4/A:151,195,221,500
88 atoms, 80 bonds, 8 residues, 2 models selected
> select #1/A:38-592 #4/A
12739 atoms, 12979 bonds, 1118 residues, 2 models selected
> ~select
Nothing selected
> select clear
> select #1/A:38-592 #4/A
12739 atoms, 12979 bonds, 1118 residues, 2 models selected
O43246 [ID: O43246] region O43246 [1-635] RMSD: 181.955
> ui tool show Matchmaker
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh
self._items_change()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change
item_names = self._item_names()
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models
ref_structures = [ref_value.structure]
^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'structure'
AttributeError: 'NoneType' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models
ref_structures = [ref_value.structure]
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 72, in refresh
self._items_change()
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 169, in _items_change
item_names = self._item_names()
^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in _item_names
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 47, in
values = [v for v in self.list_func() if self.filter_func(v)]
^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 22, in
filter_func = lambda x, ff=filter_func, cf=class_filter: ff(x) and
isinstance(x, cf)
^^^^^
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models
ref_structures = [ref_value.structure]
^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'structure'
AttributeError: 'NoneType' object has no attribute 'structure'
File
"/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/match_maker/tool.py", line 328, in _filter_bring_models
ref_structures = [ref_value.structure]
^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
> select subtract #4
8474 atoms, 8594 bonds, 555 residues, 1 model selected
> select add #4
12739 atoms, 12979 bonds, 1118 residues, 2 models selected
> close #4
> open uniprot:O43246
Summary of feedback from opening O43246 fetched from uniprot
---
notes | Alignment identifier is O43246
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to O43246 with 0 mismatches
Opened UniProt O43246
> select #1/A:38-592
8474 atoms, 8594 bonds, 555 residues, 1 model selected
> show #!1 models
> view
> select #1/A:38-592
8474 atoms, 8594 bonds, 555 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #!8 to #1/A pairing bs showAlignment true
Parameters
---
Chain pairing | bs
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with 9fqt, chain A (#8), sequence alignment score = 1397.2
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, 9fqt #8/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 117 pruned atom pairs is 1.190 angstroms; (across all 518 pairs:
9.154)
> ui tool show "Modeller Comparative"
> modeller comparative 2:1 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller"
Invalid "directory" argument: File
'/Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
model_modeller' does not exist
> ui tool show "Modeller Comparative"
> modeller comparative 2:1 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: GYL3LLFYDXWXZROT
Modeller job (ID GYL3LLFYDXWXZROT) finished
Parameters
---
Chain pairing | ss
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with chain_A, chain A (#), sequence alignment score = 1904.7
RMSD between 16 pruned atom pairs is 1.391 angstroms; (across all 556 pairs:
20.824)
Associated chain_A chain A to
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A with 0 mismatches
Chain information for chain_A
---
Chain | Description
4.1/A | No description available
Associated chain_A (4.1) chain A to O43246 with 1 mismatch
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, chain_A #4.1/A, 9fqt #8/A
> hide #!1 models
> hide #4.1 models
> show #4.1 models
> close #4
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, 9fqt #8/A
> select #1/A:421 #8/A:428
26 atoms, 24 bonds, 2 residues, 2 models selected
> ui tool show AlphaFold
> alphafold match #1
Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json
Fetching compressed AlphaFold O43246 from
https://alphafold.ebi.ac.uk/files/AF-O43246-F1-model_v4.cif
1 AlphaFold model found using sequence similarity searches: O43246 (chain A)
AlphaFold prediction matching
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
---
Chain| UniProt Id| UniProt Name| RMSD| Length| Seen| % Id
A | O43246 | CTR4_HUMAN | 9.09 | 556 | 556 | 100
Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to O43246 with 0
mismatches
Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A with 1 mismatch
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, AlphaFold CTR4_HUMAN chain A #4.1/A, 9fqt #8/A
Opened 1 AlphaFold model
> dssp #4.1
> ui tool show Matchmaker
> matchmaker #4.1 to #7 showAlignment true
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with AlphaFold CTR4_HUMAN chain A, chain A (#4.1), sequence
alignment score = 1224.4
Alignment identifier is 2
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Hiding conservation header for alignment 2
Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
#4.1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
RMSD between 286 pruned atom pairs is 1.182 angstroms; (across all 496 pairs:
5.090)
> show #!7 models
> view
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: R93DCQWMX3LHTMN8
Modeller job (ID R93DCQWMX3LHTMN8) finished
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with chain_A, chain A (#), sequence alignment score = 474
RMSD between 12 pruned atom pairs is 1.156 angstroms; (across all 489 pairs:
17.569)
Associated chain_A chain A to AlphaFold CTR4_HUMAN chain A, chain A with 0
mismatches
Chain information for chain_A
---
Chain | Description
6.1/A | No description available
Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
#4.1/A, chain_A #6.1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
fixed_noH.pdb #7/A
> hide #!7 models
> hide #!4 models
> view
> select add #1
8588 atoms, 8708 bonds, 1 pseudobond, 559 residues, 3 models selected
> select subtract #1
15 atoms, 14 bonds, 1 residue, 1 model selected
> hide #4.1 models
> view
> select add #8
11733 atoms, 11908 bonds, 1 pseudobond, 771 residues, 2 models selected
> select subtract #8
Nothing selected
> view
> select clear
> close #6
Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
#4.1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> open
> /Users/ctn700/Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
title:
Model of AF-O43246-F1_A based on AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1
[more info...]
Chain information for
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6
---
Chain | Description
A | No description available
Non-standard residues in
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6
---
CHL — (CHL)
Associated
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
chain A to AlphaFold CTR4_HUMAN chain A, chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 2: AlphaFold CTR4_HUMAN chain A
#4.1/A,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> view
> dssp #6
> show #!7 models
> ui tool show Matchmaker
> matchmaker #!7 to #6 showAlignment true
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
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A (#6) with AtCAT4_final-coot-17_H_real_space_refined_034_ARG-
fixed_noH.pdb, chain A (#7), sequence alignment score = 1294.7
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 484 pruned atom pairs is 0.363 angstroms; (across all 515 pairs:
1.488)
> ui tool show "Modeller Comparative"
> modeller comparative 1:1 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: HCW2TZFM5IIN2SBS
Modeller job (ID HCW2TZFM5IIN2SBS) finished
Parameters
---
Chain pairing | ss
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
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A (#6) with chain_A, chain A (#), sequence alignment score = 2390.7
RMSD between 188 pruned atom pairs is 0.881 angstroms; (across all 565 pairs:
9.658)
Associated chain_A chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for chain_A
---
Chain | Description
9.1/A | No description available
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
chain_A #9.1/A
> hide #6 models
> hide #!7 models
> close #9
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> select #6/A:416
22 atoms, 21 bonds, 1 residue, 1 model selected
> select #6/A:416-418
44 atoms, 43 bonds, 3 residues, 1 model selected
> select #6/A:415
17 atoms, 16 bonds, 1 residue, 1 model selected
> select #6/A:415-464
722 atoms, 734 bonds, 50 residues, 1 model selected
> delete sel
> show #!6 models
> show #!7 models
> ui tool show Matchmaker
> matchmaker #!6 to #7 showAlignment true
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A (#6), sequence alignment score = 1287.2
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 484 pruned atom pairs is 0.363 angstroms; (across all 510 pairs:
1.172)
> select clear
> ui tool show "Modeller Comparative"
> modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: F41JDLRP50L7I36W
Modeller job (ID F41JDLRP50L7I36W) finished
Parameters
---
Chain pairing | ss
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_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A (#7) with chain_A, chain A (#), sequence alignment score = 1030
RMSD between 187 pruned atom pairs is 0.807 angstroms; (across all 488 pairs:
6.590)
Associated chain_A chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for chain_A
---
Chain | Description
9.1/A | No description available
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
chain_A #9.1/A
> hide #!6 models
> hide #!7 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!6 models
> hide #!7 models
> close #9
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> select clear
> select #7/A:21
7 atoms, 7 bonds, 1 residue, 1 model selected
> select #7/A:21-582 #6/A
11760 atoms, 11956 bonds, 2 pseudobonds, 1032 residues, 4 models selected
MatchMaker Alignment [ID: 1] region AtCAT4_final-
coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain
A..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A [1-567] RMSD: 1.172
> sequence align 1 program clustalOmega
Alignment identifier is 2
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
A to AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb, chain A
with 0 mismatches
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
chain A to AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb,
chain A with 0 mismatches
Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Associated
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Webservices job id: H4DAM594BYRTK18Y
> select #1/A:473 #4.1/A:473 #6/A:473
28 atoms, 25 bonds, 3 residues, 3 models selected
> select #1/A:473 #4.1/A:473 #6/A:473
28 atoms, 25 bonds, 3 residues, 3 models selected
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: WYDGTY7T5OQLN5PB
Modeller job (ID WYDGTY7T5OQLN5PB) finished
Parameters
---
Chain pairing | ss
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
2353.4
RMSD between 150 pruned atom pairs is 0.879 angstroms; (across all 556 pairs:
11.307)
Associated Model_of_AF-O432 chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for Model_of_AF-O432
---
Chain | Description
9.1/A | No description available
Associated Model_of_AF-O432 (9.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
Model_of_AF-O432 #9.1/A
> close #9
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> sequence header 2 rmsd show
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AlphaFold CTR4_HUMAN chain A #4.1/A,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2
> show #!6 models
> show #!7 models
> hide #!7 models
> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN/AtCAT4 apo template/SLC7A4_HM_based_apo_AtCAT4_EM.pdb"
> models #6
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: I908NAOT9O4F2GS3
Modeller job (ID I908NAOT9O4F2GS3) finished
Parameters
---
Chain pairing | ss
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
2353.4
RMSD between 150 pruned atom pairs is 0.879 angstroms; (across all 556 pairs:
11.307)
Associated Model_of_AF-O432 chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for Model_of_AF-O432
---
Chain | Description
9.1/A | No description available
Associated Model_of_AF-O432 (9.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
Model_of_AF-O432 #9.1/A
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AlphaFold CTR4_HUMAN chain A #4.1/A,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A,
Model_of_AF-O432 #9.1/A
> save "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN/AtCAT4 apo template/test.pdb" models #9
> hide #!6 models
> show #5 models
> view
> close #9
Chains used in RMSD evaluation for alignment 2:
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
#1/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb #3/A,
AlphaFold CTR4_HUMAN chain A #4.1/A,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
Chains used in RMSD evaluation for alignment 1:
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb #7/A
> show #!6 models
> select add #6
8012 atoms, 8119 bonds, 1 pseudobond, 518 residues, 4 models selected
> select subtract #6
17 atoms, 15 bonds, 2 residues, 2 models selected
> select add #4.1
4219 atoms, 4338 bonds, 557 residues, 2 models selected
> select subtract #4.1
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #1
8573 atoms, 8694 bonds, 1 pseudobond, 558 residues, 2 models selected
> select subtract #1
Nothing selected
> close #6
> open "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN/AtCAT4 apo template/SLC7A4_HM_based_apo_AtCAT4_EM.pdb"
SLC7A4_HM_based_apo_AtCAT4_EM.pdb title:
Model of AF-O43246-F1_A based on AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1
[more info...]
Chain information for SLC7A4_HM_based_apo_AtCAT4_EM.pdb #6
---
Chain | Description
A | No description available
Non-standard residues in SLC7A4_HM_based_apo_AtCAT4_EM.pdb #6
---
CHL — (CHL)
> close #6
> open
> /Users/ctn700/Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
title:
Model of AF-O43246-F1_A based on AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1
[more info...]
Chain information for
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6
---
Chain | Description
A | No description available
Non-standard residues in
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6
---
CHL — (CHL)
> ui tool show Matchmaker
> matchmaker #6 to #5 showAlignment true
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A (#6), sequence alignment score = 1440.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 538 pruned atom pairs is 0.076 angstroms; (across all 556 pairs:
1.444)
> view
> select #6/A:497
16 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> ui tool show "Modeller Comparative"
> modeller comparative 1:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: WVXA273V473CHSCK
Modeller job (ID WVXA273V473CHSCK) finished
Parameters
---
Chain pairing | ss
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with chain_A, chain (blank) (#), sequence alignment score = 1079.1
RMSD between 135 pruned atom pairs is 0.924 angstroms; (across all 549 pairs:
6.141)
Associated chain_A chain to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for chain_A
---
Chain | Description
9.1/? | No description available
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, chain_A #9.1/?
> hide #5 models
> hide #6 models
> close #9
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A
> select #5/*:20
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #5/* #6/A
17117 atoms, 17326 bonds, 1129 residues, 2 models selected
MatchMaker Alignment [ID: 1] region AtCAT4 cryoEM structure in POPC-
Cholesterol in water, chain
(blank)..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A [1-573] RMSD: 1.444
> sequence align 1 program muscle
Alignment identifier is 2
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Associated pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb chain A to
AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 1
mismatch
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with
0 mismatches
Associated AtCAT4 cryoEM structure in POPC-Cholesterol in water chain (blank)
to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 0
mismatches
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
chain A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
with 0 mismatches
Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Associated
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Webservices job id: 2I19WRMM0U2SUAYT
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: Q0L10UTRKYWYBZ1C
Modeller job (ID Q0L10UTRKYWYBZ1C) finished
Modeller error output
Traceback (most recent call last):
File "ModellerModelling.py", line 80, in
a.make()
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 141, in make
self.homcsr(exit_stage)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 624, in homcsr
self.check_alignment(aln)
File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py",
line 577, in check_alignment
aln.check()
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 215, in
check
self.check_structure_structure(io=io)
File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 224, in
check_structure_structure
return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst)
_modeller.SequenceMismatchError: read_te_291E> Sequence difference between
alignment and pdb :
Modeller run output
MODELLER 10.6, 2024/10/17, r12888
PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS
Copyright(c) 1989-2024 Andrej Sali
All Rights Reserved
Written by A. Sali
with help from
B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong,
M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva,
A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov,
F. Melo, J.P. Overington, E. Feyfant
University of California, San Francisco, USA
Rockefeller University, New York, USA
Harvard University, Cambridge, USA
Imperial Cancer Research Fund, London, UK
Birkbeck College, University of London, London, UK
Kind, OS, HostName, Kernel, Processor: 4, Linux crick.cgl.ucsf.edu
4.18.0-553.62.1.el8_10.x86_64 x86_64
Date and time of compilation : 2024/10/17 20:43:03
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2025/07/28 03:41:28
environ____W> The class 'environ' is deprecated; use 'Environ' instead
openf___224_> Open $(LIB)/restyp.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups: 2
openf___224_> Open ${MODINSTALL10v6}/modlib/sstruc.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076
0.183
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592
0.183
openf___224_> Open ${MODINSTALL10v6}/modlib/resdih.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053
0.230
rdrdih__263_> Number of dihedral angle types : 9
Maximal number of dihedral angle optima: 3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open ${MODINSTALL10v6}/modlib/radii.lib
Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041
0.242
openf___224_> Open ${MODINSTALL10v6}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes: APBLE
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch.lib
rdclass_257_> Number of classes: 5
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch1.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch2.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/mnch3.lib
openf___224_> Open ${MODINSTALL10v6}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types: 21
automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead
openf___224_> Open alignment.ali
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 285887 279.187
0.273
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 303625 296.509
0.290
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 321725 314.185
0.307
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 357925 349.536
0.341
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 430325 420.239
0.410
Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 575125 561.646
0.548
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 577349 563.817 0.551
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 579605 566.021 0.553
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 581669 568.036 0.555
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 583921 570.235 0.557
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 585985 572.251 0.559
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 588205 574.419 0.561
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 590461 576.622 0.563
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 592721 578.829 0.565
read_al_374_> Non-standard residue type,position,sequence: w 580 1
read_al_374_> Non-standard residue type,position,sequence: . 1 2
read_al_374_> Non-standard residue type,position,sequence: X 566 2
read_al_374_> Non-standard residue type,position,sequence: . 1 4
read_al_374_> Non-standard residue type,position,sequence: . 565 4
read_al_374_> Non-standard residue type,position,sequence: w 580 8
Read the alignment from file : alignment.ali
Total number of alignment positions: 580
# Code #_Res #_Segm PDB_code Name
\-------------------------------------------------------------------------------
1 SLC7A4_ho 557 1 SLC7A4_homo
2 pr1000ns_ 565 1 pr1000ns_ru
3 AtCAT4_fi 517 1 AtCAT4_fina
4 AtCAT4_cr 564 1 AtCAT4_cryo
5 AtCAT4_fi 517 1 AtCAT4_fina
6 AlphaFold 556 1 AlphaFold_C
7 Model_of_ 565 1 Model_of_AF
8 Model_of_ 566 1 Model_of_AF
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open
./SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb_1.pdb
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761546 743.697
0.726
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 761546 743.697 0.726
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 761717 743.864
0.726
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 762567 744.694
0.727
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 763825 745.923
0.728
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 765729 747.782
0.730
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 765729 747.782 0.730
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 765819 747.870
0.730
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 768675 750.659
0.733
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 768675 750.659 0.733
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 768810 750.791
0.733
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 773094 754.975
0.737
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 773094 754.975 0.737
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 773292 755.168
0.737
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 779718 761.443
0.744
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 779718 761.443 0.744
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 780015 761.733
0.744
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 789637 771.130
0.753
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 789637 771.130 0.753
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 790087 771.569
0.753
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 804537 785.681
0.767
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 804537 785.681 0.767
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 805212 786.340
0.768
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 826870 807.490
0.789
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 826870 807.490 0.789
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 827878 808.475
0.790
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 860382 840.217
0.821
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 860382 840.217 0.821
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 861894 841.693
0.822
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 910650 889.307
0.868
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 910650 889.307 0.868
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 912918 891.521
0.871
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 911118 889.764
0.869
openf___224_> Open ./pr1000ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb_2.pdb
readlinef__W> File: ./pr1000ns_run1_whole_nojump_center_rotxyz-
transxyz.pdb_2.pdb, Line: 1
Modeller will only read the first 80 characters of this line.
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1082343 1056.976
1.032
read_pd_459W> Residue type ACE not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1082343 1056.976
1.032
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1082514 1057.143
1.032
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1083364 1057.973
1.033
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1084622 1059.201
1.034
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1086526 1061.061
1.036
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1086526 1061.061
1.036
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1086616 1061.148
1.036
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1089472 1063.938
1.039
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1089472 1063.938
1.039
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1089607 1064.069
1.039
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1093891 1068.253
1.043
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1093891 1068.253
1.043
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1094089 1068.446
1.043
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1100515 1074.722
1.050
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1100515 1074.722
1.050
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1100812 1075.012
1.050
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1110434 1084.408
1.059
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1110434 1084.408
1.059
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1110884 1084.848
1.059
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1125334 1098.959
1.073
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1125334 1098.959
1.073
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1126009 1099.618
1.074
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1147667 1120.769
1.095
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1147667 1120.769
1.095
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1148675 1121.753
1.095
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1181179 1153.495
1.126
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1181179 1153.495
1.126
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1182691 1154.972
1.128
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1231447 1202.585
1.174
Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 1231447 1202.585
1.174
Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 1233715 1204.800
1.177
rdpdb___459W> Residue type NME not recognized. 'AutoModel' model building
will treat this residue as a rigid body.
To use real parameters, add the residue type to ${LIB}/restyp.lib,
its topology to ${LIB}/top_*.lib, and suitable forcefield
parameters to ${LIB}/par.lib.
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 1231987 1203.112
1.175
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 565)
Alignment LLNNAX/
PDB LLNNA./
Match ***** *
Alignment residue type 24 (X, UNK) does not match pdb
residue type 68 (., NME),
for align code pr1000ns_run1_whole_nojump_center_rotxyz (atom file
pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb_2), pdb residue number "
584", chain "A"
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 2 pr1000ns_run1_whole_nojump_center_rotxyz
No output models from Modeller; see log for Modeller text output.
> delete :ACE,NME
> show #5 models
> show #6 models
> ui tool show Matchmaker
> matchmaker #6 to #5 showAlignment true
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A (#6), sequence alignment score = 1440.8
Alignment identifier is 1
Showing conservation header ("seq_conservation" residue attribute) for
alignment 1
Hiding conservation header for alignment 1
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1
RMSD between 538 pruned atom pairs is 0.076 angstroms; (across all 556 pairs:
1.444)
> select #5/*:21
14 atoms, 14 bonds, 1 residue, 1 model selected
> select #5/* #6/A
17105 atoms, 17314 bonds, 1127 residues, 2 models selected
MatchMaker Alignment [ID: 1] region AtCAT4 cryoEM structure in POPC-
Cholesterol in water, chain
(blank)..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A [2-572] RMSD: 1.444
> sequence align 1 program muscle
Alignment identifier is 2
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Associated pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb chain A to
AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 1
mismatch
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with
0 mismatches
Associated AtCAT4 cryoEM structure in POPC-Cholesterol in water chain (blank)
to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank) with 0
mismatches
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
chain A to AtCAT4 cryoEM structure in POPC-Cholesterol in water, chain (blank)
with 0 mismatches
Associated AlphaFold CTR4_HUMAN chain A (4.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Associated
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Showing conservation header ("seq_conservation" residue attribute) for
alignment 2
Webservices job id: XA5T2F4O3417BWXW
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: TD16QG7CO0YGYIPG
Modeller job (ID TD16QG7CO0YGYIPG) finished
Parameters
---
Chain pairing | ss
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
2450
RMSD between 90 pruned atom pairs is 0.789 angstroms; (across all 556 pairs:
9.819)
Associated Model_of_AF-O432 chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for Model_of_AF-O432
---
Chain | Description
9.1/A | No description available
Associated Model_of_AF-O432 (9.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, Model_of_AF-O432 #9.1/A
> hide #6 models
> hide #5 models
> hide #9.1 models
> show #9.1 models
> view
> matchmaker #9 to #5
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with Model_of_AF-O432, chain A (#9.1), sequence alignment score = 1083.3
RMSD between 133 pruned atom pairs is 0.829 angstroms; (across all 543 pairs:
9.086)
> view
> show #5 models
> select clear
> select #1/A:99 #2/A:90 #3/A:90 #4.1/A:99 #5/?:90 #6/A:99 #7/A:90 #9.1/A:70
77 atoms, 69 bonds, 8 residues, 8 models selected
> select #6/A:30-37,593-594 #9.1/A:1-8,564-565 #4.1/A:593
263 atoms, 258 bonds, 21 residues, 3 models selected
> close #9
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A
> select clear
> select #2/A #3/A:21-582 #5/* #7/A:21-582 #1/A:38-592 #4.1/A #6/A
49904 atoms, 50628 bonds, 2 pseudobonds, 3835 residues, 9 models selected
MUSCLE Realignment of MatchMaker Alignment [ID: 2] region AtCAT4 cryoEM
structure in POPC-Cholesterol in water, chain
(blank)..Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A [1-578] RMSD: 137.214
> sequence align 2 program clustalOmega replace true
Webservices job id: PAFA5I3BRFITLR34
> ui tool show "Modeller Comparative"
> modeller comparative 2:2 numModels 5 fast true multichain false hetPreserve
> false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: V898UGAC0RRASVGL
Modeller job (ID V898UGAC0RRASVGL) finished
Parameters
---
Chain pairing | ss
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with Model_of_AF-O432, chain A (#), sequence alignment score =
2436.2
RMSD between 90 pruned atom pairs is 0.812 angstroms; (across all 556 pairs:
11.736)
Associated Model_of_AF-O432 chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chain information for Model_of_AF-O432
---
Chain | Description
9.1/A | No description available
Associated Model_of_AF-O432 (9.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, Model_of_AF-O432 #9.1/A
> matchmaker #9 to #5
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 cryoEM structure in POPC-Cholesterol in water, chain (blank)
(#5) with Model_of_AF-O432, chain A (#9.1), sequence alignment score = 1097.6
RMSD between 126 pruned atom pairs is 0.780 angstroms; (across all 541 pairs:
10.794)
> hide #5 models
> open "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/sequence alignments whole
> family/alignment.praln"
Unrecognized file suffix '.praln'
> open "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/sequence alignments whole
> family/alignment.fasta"
Summary of feedback from opening /Users/ctn700/Library/CloudStorage/OneDrive-
Nexus365/SLC7_shared_DK/SLC7A4_paper_all/sequence alignments whole
family/alignment.fasta
---
notes | Alignment identifier is alignment.fasta
Associated
SLC7A4_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb
chain A to NAME:SLC7A4_CAT4|CHAIN: with 0 mismatches
Associated pr1000ns_run1_whole_nojump_center_rotxyz-transxyz.pdb chain A to
NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_H.pdb chain
A to NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches
Associated AtCAT4 cryoEM structure in POPC-Cholesterol in water chain (blank)
to NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches
Associated AtCAT4_final-coot-17_H_real_space_refined_034_ARG-fixed_noH.pdb
chain A to NAME:A. thaliana_CAT4|CHAIN: with 0 mismatches
3 messages similar to the above omitted
Showing conservation header ("seq_conservation" residue attribute) for
alignment alignment.fasta
Opened 14 sequences from alignment.fasta
> close #9
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A
> ui tool show "Modeller Comparative"
> modeller comparative alignment.fasta:1 numModels 5 fast true multichain
> false hetPreserve false hydrogens false waterPreserve true directory
> "/Users/ctn700/Library/CloudStorage/OneDrive-
> Nexus365/SLC7_shared_DK/SLC7A4_paper_all/Structure_files/Human apo homology
> model_modeller_for SN"
Webservices job id: Z233MIUGDOLV28ED
Modeller job (ID Z233MIUGDOLV28ED) finished
Parameters
---
Chain pairing | ss
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_homologymodel_modeller_dope89705_2_preprocessed_Leu_water_5_minimized.pdb,
chain A (#1) with NAME_SLC7A4_CAT4, chain A (#), sequence alignment score =
1905.2
RMSD between 5 pruned atom pairs is 1.226 angstroms; (across all 556 pairs:
109.289)
Associated NAME_SLC7A4_CAT4 chain A to NAME:SLC7A4_CAT4|CHAIN: with 0
mismatches
Chain information for NAME_SLC7A4_CAT4
---
Chain | Description
9.1/A | No description available
Associated NAME_SLC7A4_CAT4 (9.1) chain A to
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A with 0 mismatches
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A, NAME_SLC7A4_CAT4 #9.1/A
> close #9
Chains used in RMSD evaluation for alignment 1: AtCAT4 cryoEM structure in
POPC-Cholesterol in water #5/?,
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb
#6/A
> show #!4 models
> hide #!4 models
> show #!4 models
> view
> select clear
> view
> show #4.1 models
> view
> hide #!4 models
> hide #4.1 models
> show #6 models
> show #4.1 models
> hide #6 models
> show #6 models
> hide #6 models
> matchmaker #6 to #4
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 AlphaFold CTR4_HUMAN chain A, chain A (#4.1) with
Model_of_AF-O43246-F1_A_based_on_AtCAT4_final_coot_9_IL5_grafted_CHL1_1_A-1.pdb,
chain A (#6), sequence alignment score = 2554.5
RMSD between 260 pruned atom pairs is 1.171 angstroms; (across all 556 pairs:
8.899)
> 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
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