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Opened 3 months ago

Last modified 3 months ago

#18318 closed defect

ChimeraX bug report submission — at Initial Version

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

Description

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.10.dev202503131841 (2025-03-13 18:41:17 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.pyWindows fatal exception: code 0x8001010e

", line Windows fatal exception: code 0x8001010e

114 in Windows fatal exception: code 0x8001010e

worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975Windows fatal exception:  in code 0xrun
  File "8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 

1038 in _bootstrap_inner
Windows fatal exception: code 0x8001010e

  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975Windows fatal exception: code 0x8001010e

 in run
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_innerWindows fatal exception: code 0x8001010e


  File "Windows fatal exception: code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py8001010e

", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
Windows fatal exception:   File code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in Windows fatal exception: code 0x8001010e

worker
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

, line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in _bootstrap_innercode 0x
  File 8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 995Windows fatal exception: code 0x8001010e

 in _bootstrap
Windows fatal exception: code 0x8001010e


Thread 0x00000aa4 (most recent call first):
  File "Windows fatal exception: C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995

 in _bootstrap

Thread 0x00005250 (most recent call first):
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"code 0x, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"8001010e, line 975 in 

run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File Windows fatal exception: "code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrapWindows fatal exception: 
code 0x
Thread 0x00001e18 (most recent call first):
  File 8001010e"

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line Windows fatal exception: code 0x8001010e

114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edcWindows fatal exception: code 0x8001010e (most recent call first):
  File "

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in Windows fatal exception: code 0x8001010e

_exhaustive_wait
Windows fatal exception: code 0x8001010e

  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py"Windows fatal exception: code 0x8001010e, line 

878 in Windows fatal exception: code 0x8001010e

wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: , line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"code 0x8001010e

, line Windows fatal exception: code 0x8001010e

975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in code 0x8001010e

_bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x, line 114 in 8001010eworker
  File 

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 975 in Windows fatal exception: code 0x8001010e

run
  File Windows fatal exception: code 0x8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x, line 1038 in 8001010e_bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap



Thread 0x00003a9c (most recent call first):
Windows fatal exception: code 0x8001010e

  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File Windows fatal exception: "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"code 0x, line 975 in run
  File "8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
code 0x  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"8001010e, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975

 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
code 0x  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 9758001010e

 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File Windows fatal exception: code 0x8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py"Windows fatal exception: code 0x8001010e

, line 416 in get_command
  File Windows fatal exception: code 0x8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: , line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"code 0x8001010e

Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 

1038Windows fatal exception:  in code 0x8001010e_bootstrap_inner


  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "Windows fatal exception: code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py8001010e"

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

, line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in _bootstrap_innercode 0x
8001010e8001010e



  File Windows fatal exception: Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py8001010e

"code 0x, line 8001010e

Windows fatal exception: Windows fatal exception: code 0x9958001010e in _bootstrap



Thread 0x00003df4 (most recent call first):
Windows fatal exception:   File "code 0x8001010ecode 0x

8001010eWindows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e



code 0x8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py

Windows fatal exception: "Windows fatal exception: code 0xWindows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

code 0xWindows fatal exception: code 0x8001010e

114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap
8001010e

8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x
Thread 0x8001010e00000aa4 (most recent call first):


  File "Windows fatal exception: code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py8001010e

"Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e

Windows fatal exception: code 0x, line 8001010e

114 in Windows fatal exception: worker
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"code 0x, line code 0x975 in run
8001010e  File "8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x, line 1038

 in _bootstrap_inner
  File "Windows fatal exception: 8001010ecode 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"

, line 995 in _bootstrap
Windows fatal exception: code 0x8001010e


Thread 0x00005250 (most recent call first):
  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py

", line Windows fatal exception: code 0x8001010e

114 in Windows fatal exception: code 0xWindows fatal exception: code 0xworker
  File 8001010e

"8001010eWindows fatal exception: 

code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"8001010e, line 1038 in _bootstrap_inner
  File "Windows fatal exception: C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.pycode 0x8001010e

Windows fatal exception: code 0x"8001010e, line 995 in Windows fatal exception: _bootstrap

Thread 0x

00001e18 (most recent call first):
  File code 0xWindows fatal exception: code 0x8001010e



"Windows fatal exception: C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.pycode 0xWindows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File Windows fatal exception: 8001010ecode 0x8001010e

8001010e

"Windows fatal exception: code 0x8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"

Windows fatal exception: , line 1038code 0x in 8001010e

_bootstrap_inner
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap



Thread 0xWindows fatal exception: 00004a5c (most recent call first):
code 0x8001010e  File Windows fatal exception: 

code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0xcode 0x8001010e

Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010eC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py

Windows fatal exception: "Windows fatal exception: code 0x8001010ecode 0x8001010e, line 

114 in 

worker
8001010eWindows fatal exception: Windows fatal exception: code 0xcode 0x  File 8001010e

Windows fatal exception: "8001010eWindows fatal exception: 

code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.pyWindows fatal exception: code 0x"

8001010e

code 0xWindows fatal exception: code 0x8001010e

, line 8001010e

975Windows fatal exception: code 0x8001010e

8001010eWindows fatal exception: Windows fatal exception: code 0xWindows fatal exception: 

code 0xcode 0x8001010eWindows fatal exception: code 0x8001010e



8001010eWindows fatal exception: code 0x8001010e

 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"

, line 1038 in _bootstrap_inner
Windows fatal exception: code 0x  File "Windows fatal exception: C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"8001010ecode 0x8001010e8001010e

, line 

995Windows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

 in Windows fatal exception: code 0xWindows fatal exception: code 0x_bootstrap
8001010e

8001010eWindows fatal exception: 
Thread 0x000046dc (most recent call first):


  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"code 0x, line 114 in worker
  File Windows fatal exception: code 0x8001010e

8001010e

Windows fatal exception: Windows fatal exception: code 0xcode 0x8001010e

8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in code 0x_bootstrap_inner
  File 8001010e"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"

, line 995 in _bootstrapWindows fatal exception: code 0x8001010e



Thread 0xWindows fatal exception: code 0x8001010e



Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

000030d8Windows fatal exception: code 0x8001010e

 (most recent call first):
  File "code 0xC:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py"8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010eWindows fatal exception: 

code 0x8001010e, line 193Windows fatal exception:  in _from_kwarg_name_to_kwarg_name_
  File code 0x8001010e



"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.pyWindows fatal exception: code 0x8001010e

Windows fatal exception: Windows fatal exception: code 0x8001010e

code 0x8001010e"Windows fatal exception: , line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py"

, line 339 in code 0xevent_loop8001010e


  File Windows fatal exception: code 0x8001010e

"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py"Windows fatal exception: code 0x8001010e

, line 1054Windows fatal exception: code 0x8001010e

 in initWindows fatal exception: code 0x8001010e


Windows fatal exception:   File code 0x"C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py"8001010e, line 

1217 in Windows fatal exception: code 0x8001010e


  File Windows fatal exception: ""Windows fatal exception: , line 88 in code 0x_run_code
  File 8001010e""

, line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File code 0x"8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579Windows fatal exception: code 0x8001010e

 in Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

_handle_resultsWindows fatal exception: code 0x8001010e


  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: , line 531code 0x8001010e

 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in Windows fatal exception: code 0x8001010e

_bootstrap_inner
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995Windows fatal exception:  in _bootstrap

Thread 0x00002edc (most recent call first):
  File "code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py"Windows fatal exception: code 0x8001010e

, line 810 in _exhaustive_wait
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py"Windows fatal exception: code 0x8001010e

, line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x, line 522 in _handle_workers
  File "8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in Windows fatal exception: code 0x8001010e

run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"code 0x8001010e

, line Windows fatal exception: code 0x8001010e

1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap
Windows fatal exception: code 0x8001010e


Thread 0x0000543c (most recent call first):
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line Windows fatal exception: code 0x8001010e

114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

1038 in _bootstrap_inner
  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
Windows fatal exception: code 0x8001010e

  File "Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
Windows fatal exception:   File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: , line 1038 in code 0x8001010e

_bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: code 0x8001010e

, line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.pyWindows fatal exception: code 0x8001010e

", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995Windows fatal exception: code 0x8001010e

 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in workerWindows fatal exception: code 0x8001010e


  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line Windows fatal exception: code 0x8001010e

975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py"Windows fatal exception: , line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0xWindows fatal exception: code 0x8001010e

00004a5c (most recent call first):
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py"Windows fatal exception: code 0x8001010e

, line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
Windows fatal exception: code 0x8001010e

  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py"Windows fatal exception: code 0x, line 416 in 8001010e

get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in Windows fatal exception: code 0x8001010e

event_loop
Windows fatal exception: code 0x8001010e

  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py"Windows fatal exception: code 0x8001010e

, line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py"Windows fatal exception: code 0x8001010e

, line Windows fatal exception: code 0x8001010e

1217Windows fatal exception: code 0x8001010e

 in 
  File ""Windows fatal exception: code 0x8001010e

, line 88 in _run_code
  File Windows fatal exception: code 0x8001010e

"Windows fatal exception: code 0x8001010e

", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\qtpy\_utils.py", line 193 in _from_kwarg_name_to_kwarg_name_
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\gui.py", line 416 in get_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\clashes\tool.py", line 59 in run_command
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\ui\gui.py", line 339 in event_loop
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1054 in init
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\__main__.py", line 1217 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main
Windows fatal exception: code 0x8001010e

Thread 0x00004b20 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 579 in _handle_results
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b60 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 531 in _handle_tasks
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00002edc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 810 in _exhaustive_wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\connection.py", line 878 in wait
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 502 in _wait_for_updates
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 522 in _handle_workers
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000998 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004c94 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x0000543c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001f88 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000b48 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001b84 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000040c8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000ce0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001784 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003a9c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00003df4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00000aa4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00005250 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00001e18 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x00004a5c (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000046dc (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\multiprocessing\pool.py", line 114 in worker
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 975 in run
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 1038 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\threading.py", line 995 in _bootstrap

Thread 0x000030d8 (most recent call first):
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\numpy\core\_internal.py", line 282 in __init__
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\atomic\molc.py", line 334 in pointer
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\numpy\core\_methods.py", line 58 in _any
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\atomic\structure.py", line 1955 in _update_graphics_if_needed
  File "", line 720 in __ior__
  File "C:\Program Files\ChimeraX 1.10.dev202503131841\bin\Lib\site-packages\chimerax\core\triggerset.py", line 259 in _activate
  File Windows fatal exception: access violation

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010eWindows fatal exception: 

code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

Windows fatal exception: code 0x8001010e

===== Log before crash start =====
UCSF ChimeraX version: 1.10.dev202503131841 (2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\contacts\\\session_V2081.cxs

Log from Wed Jul 30 09:34:05 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\contacts\\\session_L2058.cxs

Log from Wed Jul 30 08:19:51 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\contacts\\\Contacts.cxs

Log from Tue Jul 29 15:17:34 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\emirm\\\Desktop\\\Fly\\\Chimera_WorkingFolder\\\Contacts_Modeling_Chimera\\\Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

Log from Fri Jul 25 15:41:25 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\emirm\\\Desktop\\\Fly\\\Chimera_WorkingFolder\\\Contacts_Modeling_Chimera\\\Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

Log from Fri May 2 10:11:43 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\emirm\\\Desktop\\\Fly\\\Chimera_WorkingFolder\\\Contacts_Modeling_Chimera\\\Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

Log from Wed Apr 30 15:52:46 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\Fly\\\AlphaFold\\\Chimera\\\Apt1.cxs

Log from Fri Mar 7 14:18:08 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\Users\emirm\Desktop\Fly\AlphaFold\Superpositions_hob.cxs format
> session

Log from Thu Mar 6 15:37:27 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

Log from Mon Mar 3 14:52:27 2025 Startup Messages  
---  
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  

> open
> C:/Users/emirm/Downloads/fold_2025_02_26_14_57_hob_native/fold_2025_02_26_14_57_hob_native_model_0.cif

Chain information for fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
No Surface models open  

> select add #1

18469 atoms, 18843 bonds, 2300 residues, 1 model selected  
No Surface models open  

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface style mesh

> select subtract #1

1 model selected  

> surface style dot

> color #1 cyan

> color #1 #aaff00ff

> mlp

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface style mesh

> transparency 50

> surface style solid

> color #1 red

> mlp

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> transparency 50

> surface style mesh

> cartoon style modeHelix tube sides 20

> color #1 yellow

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface #1.1: minimum, -16.90, mean -0.15, maximum 17.22  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 70

> open
> C:/Users/emirm/Downloads/fold_2025_03_03_10_24_hob_helicalcaptop/fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif

Chain information for fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #!1 models

> mlp #2

Map values for surface "fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif_A
SES surface": minimum -29.41, mean -3.659, maximum 24.89  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface style #2 mesh

> transparency #2 70

> show #!1 models

> hide #!1 models

> show #!1 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

> mmaker #2 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_2025_02_26_14_57_hob_native_model_0.cif, chain A (#1) with
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif, chain A (#2), sequence
alignment score = 11457.7  
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:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 1351 pruned atom pairs is 0.823 angstroms; (across all 2271
pairs: 20.273)  
  

> surface hidePatches

> hide #!1 models

> cartoon style #2 modeHelix tube sides 20

> show #!1 models

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\emirm/Desktop\movie2.mp4

Movie saved to C:\Users\emirm/Desktop\movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\emirm/Desktop\movie3.mp4

Movie saved to C:\Users\emirm/Desktop\movie3.mp4  
  

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> surface

> transparency 30

> surface hidePatches

> open
> C:/Users/emirm/Downloads/fold_2025_03_03_11_19_hob_l2221p/fold_2025_03_03_11_19_hob_l2221p_model_0.cif

Chain information for fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Associated fold_2025_03_03_11_19_hob_l2221p_model_0.cif chain A to
fold_2025_02_26_14_57_hob_native_model_0.cif, chain A with 1 mismatch  
Chains used in RMSD evaluation for alignment 1:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A  
Computing secondary structure  

> hide #!2 models

> mmaker #3 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_2025_02_26_14_57_hob_native_model_0.cif, chain A (#1) with
fold_2025_03_03_11_19_hob_l2221p_model_0.cif, chain A (#3), sequence alignment
score = 11719.1  
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:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 1478 pruned atom pairs is 1.025 angstroms; (across all 2300
pairs: 4.757)  
  

> hide #!1 models

> cartoon style #3 modeHelix tube sides 20

> show #!1 models

> hide #3 models

> open
> C:/Users/emirm/Downloads/fold_2025_03_03_11_19_hob_l2221ppppp/fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif

Chain information for fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Associated fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif chain A to
fold_2025_02_26_14_57_hob_native_model_0.cif, chain A with 5 mismatches  
Chains used in RMSD evaluation for alignment 1:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A,
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A  
Associated fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif chain A to
fold_2025_03_03_11_19_hob_l2221p_model_0.cif, chain A with 4 mismatches  
Chains used in RMSD evaluation for alignment 2:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A,
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A  
Computing secondary structure  

> hide #!1 models

> cartoon style #4 modeHelix tube sides 20

> show #!1 models

> mmaker #4 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_2025_02_26_14_57_hob_native_model_0.cif, chain A (#1) with
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif, chain A (#4), sequence
alignment score = 11678.5  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 1213 pruned atom pairs is 0.897 angstroms; (across all 2300
pairs: 10.567)  
  

> show #!2 models

> hide #!2 models

> show #3 models

> hide #3 models

> surface #1,4

> surface hidePatches #1,4

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

——— End of log from Mon Mar 3 14:52:27 2025 ———

opened ChimeraX session  

> hide #!4 models

> color #1 #ffff7fff

> show #!2 models

> hide #!2 models

Alignment identifier is 1/A  
Alignment identifier is 2/A  
Alignment identifier is 3/A  
Alignment identifier is 4/A  

> select #1/A:102

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:102-115

118 atoms, 118 bonds, 14 residues, 1 model selected  

> select #1/A:1972

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1972-2080

886 atoms, 899 bonds, 109 residues, 1 model selected  

> select #1/A:1972-2089

948 atoms, 962 bonds, 118 residues, 1 model selected  

> color (#!1 & sel) orange

> show sel atoms

> style sel ball

Changed 948 atom styles  

> hide sel atoms

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #1/A:2058

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #1/A:2080

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select add #1/A:2059

34 atoms, 30 bonds, 4 residues, 2 models selected  

> select add #1/A:2057

41 atoms, 36 bonds, 5 residues, 2 models selected  

> select add #1/A:2082

46 atoms, 40 bonds, 6 residues, 2 models selected  

> select add #1/A:2021

55 atoms, 48 bonds, 7 residues, 2 models selected  

> select add #1/A:2022

63 atoms, 55 bonds, 8 residues, 2 models selected  

> select add #1/A:2023

67 atoms, 58 bonds, 9 residues, 2 models selected  

> select add #1/A:2056

78 atoms, 68 bonds, 10 residues, 2 models selected  

> show sel atoms

> color bfactor sel

78 atoms, 10 residues, 1 surfaces, atom bfactor range 42.9 to 88.1  

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

78 atoms, 10 residues, 1 surfaces, atom bfactor range 42.9 to 88.1  

> color bfactor sel

78 atoms, 10 residues, 1 surfaces, atom bfactor range 42.9 to 88.1  

> hide sel surfaces

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> ui tool show Contacts

Restriction atom specifier must not be blank  

> contacts sel saveFile C:/Users/emirm/Desktop/Contacts_trial restrict both
> intraRes true ignoreHiddenModels true select true color #6a6a6a dashes 5
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    36 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.731    2.789
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.496    2.994
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.469    2.561
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   0.445    2.215
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.084    2.946
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.067    3.453
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    0.039    3.721
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.025    3.495
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2   -0.046    2.706
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.178    3.478
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   -0.211    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CB    -0.284    4.044
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.318    3.618
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE    -0.359    3.019
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    -0.391    4.151
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
36 contacts  

> contacts sel saveFile C:/Users/emirm/Desktop/Contacts_trial2 restrict both
> intraRes true ignoreHiddenModels true select true color #6a6a6a dashes 5
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    36 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.731    2.789
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.496    2.994
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.469    2.561
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   0.445    2.215
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.084    2.946
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.067    3.453
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    0.039    3.721
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.025    3.495
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2   -0.046    2.706
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.178    3.478
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   -0.211    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CB    -0.284    4.044
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.318    3.618
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE    -0.359    3.019
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    -0.391    4.151
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
36 contacts  

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/emirm/Desktop/H-bonds_trial dashes 4 restrict
> both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    5 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
5 hydrogen bonds found  

> hbonds sel saveFile C:/Users/emirm/Desktop/H-bonds_trial2 dashes 4 restrict
> both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    5 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
5 hydrogen bonds found  

> hide #1.2 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

——— End of log from Thu Mar 6 15:37:27 2025 ———

opened ChimeraX session  

> select #2/A:16-17

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #2/A:16-17

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #1/A:2056

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

> select #1/A:2056-2102

379 atoms, 388 bonds, 17 pseudobonds, 47 residues, 3 models selected  

> select #1/A:2055

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

> select #1/A:1961-2055

766 atoms, 775 bonds, 95 residues, 1 model selected  

> color (#!1 & sel) #ffff7fff

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6684 atoms, 6718 bonds, 15 pseudobonds, 812 residues, 3 models selected  

> select #1/A:2056

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

> select #1/A:2056-2102

379 atoms, 388 bonds, 17 pseudobonds, 47 residues, 3 models selected  

> color (#!1 & sel) orange

> select #1/A:2055

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

> select #1/A:1990-2055

525 atoms, 531 bonds, 66 residues, 1 model selected  

> color #1 white

> color #1 #8b8b8bff

> color #1 #cfcfcfff

> select #1/A:2056

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

> select #1/A:2056-2102

379 atoms, 388 bonds, 17 pseudobonds, 47 residues, 3 models selected  

> color (#!1 & sel) orange

> select #1/A:2042

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:2020-2042

191 atoms, 192 bonds, 23 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> select #1/A:2176

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

> select #1/A:2176-2194

159 atoms, 163 bonds, 19 residues, 1 model selected  

> color (#!1 & sel) hot pink

> select #1/A:2198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2198-2238

343 atoms, 351 bonds, 41 residues, 1 model selected  

> color (#!1 & sel) purple

> hide #1.3 models

> select subtract #1.1

1 model selected  

> hide #1.1 models

> select add #1.1

18469 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> select #1/A:2198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2198-2238

343 atoms, 351 bonds, 41 residues, 1 model selected  

> color (#!1 & sel) lime

> select subtract #1.1

1 model selected  

> select add #1

18469 atoms, 18843 bonds, 41 pseudobonds, 2300 residues, 3 models selected  

> hide sel atoms

> hide #!1 models

> show #!1 models

> select subtract #1.1

1 model selected  

> select add #1.2

36 pseudobonds, 1 model selected  

> save C:\Users\emirm/Desktop\image1.png supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole.png width 816 height
> 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole.tif width 816 height
> 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole_180.tif width 816
> height 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole.tif width 816 height
> 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1.tif width 816 height
> 443 supersample 3

> select add #1/A:2020

8 atoms, 7 bonds, 36 pseudobonds, 1 residue, 2 models selected  

> select add #1/A:2021

17 atoms, 15 bonds, 36 pseudobonds, 2 residues, 3 models selected  

> select add #1/A:2022

25 atoms, 22 bonds, 36 pseudobonds, 3 residues, 3 models selected  

> select add #1/A:2060

33 atoms, 29 bonds, 36 pseudobonds, 4 residues, 3 models selected  

> select add #1/A:2059

44 atoms, 39 bonds, 36 pseudobonds, 5 residues, 3 models selected  

> select add #1/A:2058

52 atoms, 46 bonds, 36 pseudobonds, 6 residues, 3 models selected  

> select add #1/A:2078

61 atoms, 54 bonds, 36 pseudobonds, 7 residues, 3 models selected  

> select add #1/A:2079

69 atoms, 61 bonds, 36 pseudobonds, 8 residues, 3 models selected  

> select add #1/A:2080

77 atoms, 68 bonds, 36 pseudobonds, 9 residues, 3 models selected  

> select add #1/A:2081

84 atoms, 74 bonds, 36 pseudobonds, 10 residues, 3 models selected  

> select subtract #1/A:2078

75 atoms, 66 bonds, 36 pseudobonds, 9 residues, 3 models selected  

> select add #1/A:2082

80 atoms, 70 bonds, 36 pseudobonds, 10 residues, 3 models selected  

> select add #1/A:2056

91 atoms, 80 bonds, 36 pseudobonds, 11 residues, 3 models selected  

> select add #1/A:2023

95 atoms, 83 bonds, 36 pseudobonds, 12 residues, 3 models selected  

> select add #1/A:2057

102 atoms, 89 bonds, 36 pseudobonds, 13 residues, 3 models selected  

> select subtract #1/A:2056

91 atoms, 79 bonds, 21 pseudobonds, 12 residues, 3 models selected  

> show sel atoms

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

91 atoms, 12 residues, 1 surfaces, atom bfactor range 51.2 to 89.1  

> hide sel surfaces

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues.tif width
> 816 height 443 supersample 3

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_contacts restrict both
> intraRes true ignoreHiddenModels true select true color #6a6a6a dashes 4
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    31 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     0.034    3.266
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2   -0.044    3.804
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2   -0.059    3.579
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.157    2.817
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.189    3.949
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N     -0.197    2.857
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.213    3.513
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.220    3.520
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.274    3.574
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 CG1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.376    4.136
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
31 contacts  

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_contacts2 restrict
> both intraRes true ignoreHiddenModels true select true color #6a6a6a dashes
> 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    31 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     0.034    3.266
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2   -0.044    3.804
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2   -0.059    3.579
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.157    2.817
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.189    3.949
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N     -0.197    2.857
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.213    3.513
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.220    3.520
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.274    3.574
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 CG1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.376    4.136
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
31 contacts  

> show #1.2 models

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_contacts.tif
> width 816 height 443 supersample 3

> show #1.3 models

> hide #1.3 models

> close #1.3

> ui tool show Distances

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_h-
> bonds dashes 4 restrict both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    7 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O  no hydrogen  2.857  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O  no hydrogen  2.817  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
7 hydrogen bonds found  

> hbonds sel saveFile C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_h-
> bonds2 dashes 4 restrict both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    7 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O  no hydrogen  2.857  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O  no hydrogen  2.817  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
7 hydrogen bonds found  

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_h-bonds.tif
> width 778 height 443 supersample 3

> hide #1.3 models

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_clashes restrict both
> ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: False
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_clashes2 restrict both
> ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: False
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> hide #1.4 models

> show #1.4 models

> select subtract #1.4

39 atoms, 12 residues, 2 models selected  

> hide #1.4 models

> select subtract #1.4

39 atoms, 12 residues, 2 models selected  

> show #1.4 models

> hide #1.4 models

> select subtract #1.4

39 atoms, 12 residues, 2 models selected  

> ui tool show Angles/Torsions

> ui tool show "Check Waters"

QWindowsWindow::setMouseGrabEnabled: Not setting mouse grab for invisible
window QWidgetWindow/'QMenuClassWindow'  

[Repeated 4 time(s)]

> hbonds interModel false reveal true restrict any name "water H-bonds"

7487 hydrogen bonds found  

> ~select

Nothing selected  

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> show #1.5 models

> select add #1.5

1868 pseudobonds, 1 model selected  

> hide #1.5 models

> show #1.5 models

> select subtract #1.5

Nothing selected  

> hide #1.5 models

> hide #!1 atoms

> select add #1.1

18469 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> select add #1.2

31 pseudobonds, 1 model selected  

> select subtract #1.2

Nothing selected  

> select add #1.2

31 pseudobonds, 1 model selected  

> select subtract #1.2

Nothing selected  

> show #1.2 models

> select add #1.2

31 pseudobonds, 1 model selected  

> show #!1 atoms

[Repeated 1 time(s)]

> hide #!1 atoms

> hide #1.2 models

> select subtract #1.2

Nothing selected  

> select subtract #1.4

Nothing selected  

> select #1/A:2020

8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/A:2020-2023

29 atoms, 28 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2020-2023,2057-2060

63 atoms, 61 bonds, 24 pseudobonds, 8 residues, 4 models selected  

> select #1/A:2020-2023,2057-2060,2079-2082

91 atoms, 88 bonds, 46 pseudobonds, 12 residues, 4 models selected  

> style sel ball

Changed 91 atom styles  

> show sel atoms

> select subtract #1.1

1 model selected  

> select add #1.2

31 pseudobonds, 1 model selected  

> select add #1.3

38 pseudobonds, 2 models selected  

> select subtract #1.4

38 pseudobonds, 2 models selected  

> select subtract #1.3

31 pseudobonds, 1 model selected  

> select subtract #1.2

Nothing selected  

> select subtract #1.4

Nothing selected  

> show #1.2 models

> log metadata #1

No models had metadata

> log chains #1

Chain information for fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> select add #1.2

31 pseudobonds, 1 model selected  

> log metadata #1

No models had metadata

> log chains #1

Chain information for fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> interfaces #!1 & ~solvent

0 buried areas:  

> ui tool show Contacts

> help help:user/tools/clashes.html

> select subtract #1.2

Nothing selected  

> select subtract #1.4

Nothing selected  

> hide #1.2 models

> select #1/A:2055

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

> select add #1/A:2054

19 atoms, 18 bonds, 2 residues, 2 models selected  

> hide sel cartoons

> select #1/A:1618

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

> select #1/A:1619

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/A:1618

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

> select add #1/A:1619

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #1/A:1620

26 atoms, 23 bonds, 3 residues, 2 models selected  

> hide sel cartoons

> select add #1/A:1617

33 atoms, 29 bonds, 4 residues, 2 models selected  

> select add #1/A:1615

43 atoms, 39 bonds, 5 residues, 2 models selected  

> select add #1/A:1616

49 atoms, 44 bonds, 6 residues, 2 models selected  

> hide sel cartoons

> select add #1/A:2053

56 atoms, 50 bonds, 7 residues, 2 models selected  

> select add #1/A:2052

64 atoms, 57 bonds, 8 residues, 2 models selected  

> hide sel cartoons

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues.tif width
> 778 height 443 supersample 3

> show #1.2 models

> select add #1/A:2056

75 atoms, 67 bonds, 9 residues, 2 models selected  

> hide sel cartoons

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues.tif width
> 778 height 443 supersample 3

> show #1.2 models

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_contacts.tif
> width 778 height 443 supersample 3

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.3 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_h-bonds.tif
> width 778 height 443 supersample 3

> show #1.2 models

> hide #1.2 models

> hide #1.3 models

> color #1.4 yellow models

> show #1.4 models

> hide #1.4 models

> show #1.5 models

> hide #1.5 models

> select subtract #1.4

75 atoms, 67 bonds, 9 residues, 2 models selected  

> select #1/A:2020

8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/A:2020-2023

29 atoms, 28 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2057-2058

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/A:2057-2060

34 atoms, 33 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2020-2023,2057-2060

63 atoms, 61 bonds, 24 pseudobonds, 8 residues, 4 models selected  

> select #1/A:2020-2023,2057-2060,2079-2082

91 atoms, 88 bonds, 46 pseudobonds, 12 residues, 4 models selected  

> coulombic sel

Coulombic values for fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface #1.1: minimum, -16.90, mean -0.15, maximum 17.22  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> save C:\Users\emirm/Desktop\image2.png supersample 3

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_hydrophobicity.tif
> width 778 height 443 supersample 3

> volume style mesh

No volumes specified  

> surface style #1 mesh

> surface (#!1 & sel)

> transparency (#!1 & sel) 50

> select subtract #1.1

1 model selected  

> select add #1.1

18469 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> transparency #1.1#!1 20

> transparency #1.1#!1 0

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_hydrophobicity_mesh.tif
> width 778 height 443 supersample 3

> ui tool show "Color Actions"

> color byhetero

> color byelement

> color byhetero

[Repeated 1 time(s)]

> color bynucleotide

> color bychain

> undo

[Repeated 6 time(s)]

> redo

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

> ui tool show "Color Actions"

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.9-cp311-cp311-win_amd64.whl  
Downloading bundle SEQCROW-1.8.18-py3-none-any.whl  
Installed SEQCROW (1.8.18)  

> select #1/A:2059

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

> select #1/A:2059

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

> help help:user/tools/sequenceviewer.html#copy

> toolshed show

> help help:quickstart

> help help:user

> swapaa /L:2058 pro

No amino acid residues specified for swapping  

> swapaa /L:2058P

Missing or invalid "resTypes" argument: Expected a text string  

> ui tool show Rotamers

[Repeated 1 time(s)]

> swapaa interactive sel ARG rotLib Dunbrack

fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059: phi -132.9, psi
123.6 trans  
Changed 600 bond radii  

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6684 atoms, 6718 bonds, 825 pseudobonds, 812 residues, 4 models selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel LEU rotLib Dunbrack

fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058: phi -137.9, psi
132.6 trans  
Changed 45 bond radii  

> hbonds #!1 & ~#!1/A:2058 & ~solvent reveal true restrict #1.6 & ~@c,ca,n

0 hydrogen bonds found  

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6684 atoms, 6718 bonds, 820 pseudobonds, 812 residues, 3 models selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> swapaa

Missing or invalid "residues" argument: empty atom specifier  

> redo

> select #1/A:2020-2023,2057-2060,2079-2082

91 atoms, 88 bonds, 39 pseudobonds, 12 residues, 3 models selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> swapaa /A:2058 leu to A:2058 val

Expected ',' or a keyword  

> swapaa /A:2058 leu A:2058 val

Expected ',' or a keyword  

> swapaa /A:L2058V

Missing or invalid "resTypes" argument: Expected a text string  

> swapaa /A:2058 val

Using Dunbrack library  
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058: phi -137.9, psi
132.6 trans  
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A LEU 2058: phi -139.1,
psi 132.6 trans  
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A LEU 2058: phi -138.8, psi
132.1 trans  
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A LEU 2058: phi -136.2,
psi 130.5 trans  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2058  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A VAL 2058  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A VAL 2058  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A VAL 2058  

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6683 atoms, 6717 bonds, 815 pseudobonds, 812 residues, 3 models selected  

> swapaa /A:2058 pro

Using Dunbrack library  
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2058: phi -137.9, psi
132.6 trans  
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A VAL 2058: phi -139.1,
psi 132.6 trans  
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A VAL 2058: phi -138.8, psi
132.1 trans  
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A VAL 2058: phi -136.2,
psi 130.5 trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A PRO 2058  
Applying PRO rotamer (chi angles: 27.3 -34.5) to
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A PRO 2058  
Applying PRO rotamer (chi angles: 27.3 -34.5) to
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A PRO 2058  
Applying PRO rotamer (chi angles: -25.1 36.3) to
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A PRO 2058  

> select
> #1/A:2-32,134-142,212-214,256-268,291-300,402-420,458-463,513-519,588-605,696-698,737-756,841-849,878-896,929-965,971-998,1022-1024,1027-1037,1142-1144,1146-1158,1171-1178,1275-1277,1325-1339,1349-1351,1361-1363,1490-1497,1515-1538,1595-1604,1618-1623,1625-1631,1712-1714,1720-1722,1737-1739,1793-1795,1834-1848,1853-1871,1874-1911,1916-1958,2090-2100,2111-2113,2162-2172,2220-2247,2262-2271

4475 atoms, 4510 bonds, 460 pseudobonds, 539 residues, 2 models selected  

> select #1/A:2020

8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/A:2020-2023

29 atoms, 28 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:2057-2060

33 atoms, 33 bonds, 4 residues, 1 model selected  

> select #1/A:2078-2079

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:2078-2082

37 atoms, 36 bonds, 4 pseudobonds, 5 residues, 3 models selected  

> select #1/A:2079

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2079-2082

28 atoms, 27 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2057-2060,2079-2082

61 atoms, 60 bonds, 17 pseudobonds, 8 residues, 3 models selected  

> select #1/A:2020-2023,2057-2060,2079-2082

90 atoms, 88 bonds, 34 pseudobonds, 12 residues, 3 models selected  

> hide sel surfaces

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_L2058P.tif
> width 778 height 443 supersample 3

> select subtract #1.1

3 atoms, 2 bonds, 1 residue, 2 models selected  

> select subtract #1.4

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

> show #1.2 models

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_L2058P_contacts.tif
> width 778 height 443 supersample 3

> show #1.5 models

> hide #1.2 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> select add #1.5

3 atoms, 2 bonds, 1868 pseudobonds, 1 residue, 2 models selected  

> select subtract #1.5

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

> show #1.5 models

> hide #1.5 models

> show #1.4 models

> select subtract #1.4

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

> hide #1.4 models

> show #1.2 models

> hide #1.2 models

> show #1.5 models

> hide #1.5 models

> close #1.5

> select #1/A:2020-2023,2057-2060,2079-2082

90 atoms, 88 bonds, 26 pseudobonds, 12 residues, 2 models selected  

> select #1/A:2020-2023,2057-2061,2079-2082

101 atoms, 100 bonds, 26 pseudobonds, 13 residues, 2 models selected  

> select #1/A:2020-2023,2057-2061,2079-2082

101 atoms, 100 bonds, 26 pseudobonds, 13 residues, 2 models selected  

> select #1/A:2020-2023,2057-2061,2079-2082

101 atoms, 100 bonds, 26 pseudobonds, 13 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel dashes 4 restrict both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    7 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O  no hydrogen  2.857  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A PRO 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O  no hydrogen  2.817  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
7 hydrogen bonds found  

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_L2058P_h-
> bonds.tif width 778 height 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

> show #!2 models

> show #!3 models

> close #2-4

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

[Repeated 1 time(s)]

——— End of log from Fri Mar 7 14:18:08 2025 ———

> view name session-start

opened ChimeraX session  

> select
> /A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6683 atoms, 6718 bonds, 22 pseudobonds, 812 residues, 3 models selected  

> select /A:2151-2152

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:2151-2152

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select
> /A:2-32,134-142,212-214,256-268,291-300,402-420,458-463,513-519,588-605,696-698,737-756,841-849,878-896,929-965,971-998,1022-1024,1027-1037,1142-1144,1146-1158,1171-1178,1275-1277,1325-1339,1349-1351,1361-1363,1490-1497,1515-1538,1595-1604,1618-1623,1625-1631,1712-1714,1720-1722,1737-1739,1793-1795,1834-1848,1853-1871,1874-1911,1916-1958,2090-2100,2111-2113,2162-2172,2220-2247,2262-2271

4475 atoms, 4510 bonds, 539 residues, 1 model selected  

> select
> /A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6683 atoms, 6718 bonds, 22 pseudobonds, 812 residues, 3 models selected  

> select /A:2050

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2050-2100

408 atoms, 418 bonds, 17 pseudobonds, 51 residues, 3 models selected  

> select /A:1831

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:1831-2300

3800 atoms, 3854 bonds, 33 pseudobonds, 470 residues, 3 models selected  

> show sel atoms

[Repeated 1 time(s)]

> style (#!1 & sel) stick

Changed 3800 atom styles  

> select /A:2027

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2027-2091

523 atoms, 532 bonds, 17 pseudobonds, 65 residues, 3 models selected  

> select /A:2273-2300

220 atoms, 221 bonds, 28 residues, 1 model selected  

> select /A:1711-2300

4727 atoms, 4803 bonds, 33 pseudobonds, 590 residues, 3 models selected  

> hide sel atoms

> hide #!1 models

> show #!1 models

> close #1.1-4

> select subtract /A:2020

4719 atoms, 4794 bonds, 589 residues, 1 model selected  

> select subtract /A:2021

4710 atoms, 4785 bonds, 588 residues, 1 model selected  

> select add #1

18468 atoms, 18843 bonds, 2300 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /A:2021

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select subtract /A:2021

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /A:2021

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:2022

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select add /A:2023

29 atoms, 25 bonds, 4 residues, 1 model selected  

> color sel cornflower blue

> select /A:2159

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

> select /A:2156-2159

33 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A:2056

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

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> color sel orange

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1938

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1938

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1923

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1923-2300

3033 atoms, 3079 bonds, 378 residues, 1 model selected  

> show sel cartoons

> select /A:1787

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

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1787-1852

524 atoms, 538 bonds, 66 residues, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2040-2102

505 atoms, 517 bonds, 63 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2040-2102

505 atoms, 517 bonds, 63 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2040

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2040-2055

127 atoms, 128 bonds, 16 residues, 1 model selected  

> select /A:2040-2055,2180-2188

199 atoms, 201 bonds, 25 residues, 1 model selected  

> select /A:2020-2026,2040-2055,2180-2188

255 atoms, 256 bonds, 32 residues, 1 model selected  

> select /A:2058

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2236

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

> select /A:2205-2236

268 atoms, 275 bonds, 32 residues, 1 model selected  

> select /A:2125

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:2125

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:2056

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

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select
> /A:2-32,134-142,212-214,256-268,291-300,402-420,458-463,513-519,588-605,696-698,737-756,841-849,878-896,929-965,971-998,1022-1024,1027-1037,1142-1144,1146-1158,1171-1178,1275-1277,1325-1339,1349-1351,1361-1363,1490-1497,1515-1538,1595-1604,1618-1623,1625-1631,1712-1714,1720-1722,1737-1739,1793-1795,1834-1848,1853-1871,1874-1911,1916-1958,2090-2100,2111-2113,2162-2172,2220-2247,2262-2271

4475 atoms, 4510 bonds, 539 residues, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2126

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2126

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2184

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2184-2187

32 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2021

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2027

64 atoms, 63 bonds, 8 residues, 1 model selected  

> select /A:2003-2040,2056-2102

694 atoms, 708 bonds, 85 residues, 1 model selected  

> select /A:2054-2055

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:2003-2040,2056-2102

694 atoms, 708 bonds, 85 residues, 1 model selected  

> select /A:2050-2055

48 atoms, 49 bonds, 6 residues, 1 model selected  

> select /A:2178

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

> select /A:2176-2178

31 atoms, 32 bonds, 3 residues, 1 model selected  

> select /A:2055-2056

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:2040-2056

138 atoms, 139 bonds, 17 residues, 1 model selected  

> select /A:2020-2028,2040-2056

211 atoms, 211 bonds, 26 residues, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2275-2300

208 atoms, 209 bonds, 26 residues, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2275-2300

208 atoms, 209 bonds, 26 residues, 1 model selected  

> select /A:2127

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2127-2157

231 atoms, 232 bonds, 31 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2020-2188

1342 atoms, 1362 bonds, 169 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2020-2027

64 atoms, 63 bonds, 8 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2200-2201

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2200-2203

31 atoms, 30 bonds, 4 residues, 1 model selected  

> select /A:2064

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

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2064-2094

239 atoms, 244 bonds, 31 residues, 1 model selected  

> select /A:2213-2214

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

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2213-2215

30 atoms, 31 bonds, 3 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> swapaa /A: 2058 leu

Using Dunbrack library  
/A PRO 2058: phi -137.9, psi 132.6 trans  
Applying LEU rotamer (chi angles: 177.6 65.4) to /A LEU 2058  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select /A:2300

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:2299-2300

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2300

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:2300

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

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_clashes.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    238 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.121    3.639
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A ILE 2084 CD1  /A ILE 2086 CG1   -0.021    3.781
    /A ILE 2084 CG2  /A ALA 2082 O     -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A ILE 2084 CD1  /A LEU 2040 CD1   -0.076    3.836
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A ILE 2084 CG2  /A PRO 2083 O     -0.162    3.462
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.197    3.957
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CB   /A LEU 2041 O     -0.256    3.556
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A VAL 2081 CG1  /A ILE 2084 CD1   -0.266    4.026
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.313    4.073
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A VAL 2073 CG2  /A VAL 2068 CG2   -0.328    4.088
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
238 contacts  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #1.1 models

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_contacts.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> hide #1.2 models

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 291 pseudobonds, 81 residues, 4 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_hbonds.png
> width 701 height 491 supersample 3

> hide #1.3 models

> show #1.1 models

> close #1.1-3

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> hide sel atoms

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> swapaa /A: 2068 leu

Using Dunbrack library  
/A VAL 2068: phi -108.3, psi 119.0 trans  
Applying LEU rotamer (chi angles: 177.4 64.0) to /A LEU 2068  

> ui tool show Clashes

[Repeated 1 time(s)]

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:1801-1802

14 atoms, 15 bonds, 2 residues, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_clashes.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> ui tool show Distances

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    238 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.121    3.639
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A ILE 2084 CD1  /A ILE 2086 CG1   -0.021    3.781
    /A ILE 2084 CG2  /A ALA 2082 O     -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A ILE 2084 CD1  /A LEU 2040 CD1   -0.076    3.836
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2068 CD1  /A GLY 2069 N     -0.084    3.604
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A ILE 2084 CG2  /A PRO 2083 O     -0.162    3.462
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.197    3.957
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CB   /A LEU 2041 O     -0.256    3.556
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A VAL 2081 CG1  /A ILE 2084 CD1   -0.266    4.026
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.313    4.073
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A LEU 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
238 contacts  

> hide #!1 models

> show #!1 models

> hide #1.1 models

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_contacts.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A LEU 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A LEU 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> hide #1.2 models

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 291 pseudobonds, 81 residues, 4 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_hbonds.png
> width 701 height 491 supersample 3

> swapaa /A: 2068 val

Using Dunbrack library  
/A LEU 2068: phi -108.3, psi 119.0 trans  
Applying VAL rotamer (chi angles: 178.6) to /A VAL 2068  

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel gray

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel orange

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel gray

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel orange

> swapaa /A: 2068 ile

Using Dunbrack library  
/A VAL 2068: phi -108.3, psi 119.0 trans  
Applying ILE rotamer (chi angles: -60.2 170.9) to /A ILE 2068  

> close #1.1-3

> select /A:2086

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 81 residues, 1 model selected  

> select /A:2086

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068I_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> select /A:2176

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

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:2176

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

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068I_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    239 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.121    3.639
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A ILE 2084 CD1  /A ILE 2086 CG1   -0.021    3.781
    /A ILE 2084 CG2  /A ALA 2082 O     -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A ILE 2084 CD1  /A LEU 2040 CD1   -0.076    3.836
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A ILE 2084 CG2  /A PRO 2083 O     -0.162    3.462
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.197    3.957
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CB   /A LEU 2041 O     -0.256    3.556
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A VAL 2081 CG1  /A ILE 2084 CD1   -0.266    4.026
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A ILE 2068 CD1  /A VAL 2073 CG2   -0.309    4.069
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.313    4.073
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A ILE 2068 CG1  /A VAL 2073 CG2   -0.328    4.088
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A ILE 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
239 contacts  

> select /A:2239-2240

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 244 pseudobonds, 81 residues, 3 models selected  

> select /A:2239-2240

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 244 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068I_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A ILE 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A ILE 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> swapaa /A: 2068 val

Using Dunbrack library  
/A ILE 2068: phi -108.3, psi 119.0 trans  
Applying VAL rotamer (chi angles: 178.6) to /A VAL 2068  

> close #1.1-3

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084-2085

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2084-2085

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084-2085

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel orange

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel gray

> swapaa /A: 2084 val

Using Dunbrack library  
/A ILE 2084: phi -131.8, psi 148.9 trans  
Applying VAL rotamer (chi angles: -62.5) to /A VAL 2084  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 661 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084V_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084V_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    236 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A ALA 2082 O    /A VAL 2084 CG1   0.205    3.095
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A VAL 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A VAL 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A VAL 2186 CG1  /A VAL 2084 CG2   -0.130    3.890
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A VAL 2084 CG1  /A PRO 2083 O     -0.138    3.438
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A VAL 2084 CG2  /A ILE 2086 CG1   -0.162    3.922
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A VAL 2084 CB   /A LEU 2041 O     -0.241    3.541
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A VAL 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A VAL 2084 CG1  /A VAL 2081 CG1   -0.314    4.074
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A ILE 2086 CD1  /A VAL 2084 CG2   -0.337    4.097
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A VAL 2068 CG2  /A VAL 2073 CG2   -0.370    4.130
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
236 contacts  

> select /A:2125-2126

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 661 bonds, 241 pseudobonds, 81 residues, 3 models selected  

> select /A:2125-2126

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 661 bonds, 241 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084V_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A VAL 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> close #1.1-3

> swapaa /A: 2084 leu

Using Dunbrack library  
/A VAL 2084: phi -131.8, psi 148.9 trans  
Applying LEU rotamer (chi angles: -61.3 171.4) to /A LEU 2084  

> select /A:2147

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2147

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> ui tool show "Check Waters"

> hbonds interModel false reveal true restrict any name "water H-bonds"

1868 hydrogen bonds found  

> ~select

Nothing selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 48 pseudobonds, 81 residues, 2 models selected  

> close #1.1

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084L_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    6 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A LEU 2084 CD2  /A ALA 2042 CA    0.625    3.135
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
6 clashes  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084L_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    243 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A ALA 2042 CA   /A LEU 2084 CD2   0.625    3.135
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A LEU 2084 CD1  /A VAL 2081 CG1   0.548    3.212
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LEU 2084 CG   /A ALA 2082 O     0.215    3.085
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A LEU 2084 CD2  /A VAL 2057 CG1   0.122    3.638
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 O    /A LEU 2084 CD2   0.032    3.268
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A ALA 2042 CB   /A LEU 2084 CD2   0.023    3.737
    /A ALA 2042 N    /A LEU 2084 CD2   0.022    3.498
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A LEU 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A LEU 2041 O    /A LEU 2084 CD2   -0.060    3.360
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A LEU 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A LEU 2084 CG   /A PRO 2083 O     -0.146    3.446
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A LEU 2084 CD2  /A LEU 2041 C     -0.168    3.658
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A PRO 2083 C    /A LEU 2084 CD2   -0.219    3.709
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A LEU 2084 CB   /A LEU 2041 O     -0.236    3.536
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A LEU 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A LEU 2084 CG   /A VAL 2081 CG1   -0.300    4.060
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A VAL 2068 CG2  /A VAL 2073 CG2   -0.370    4.130
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A LEU 2084 CD1  /A ALA 2082 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
243 contacts  

> select /A:2177

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 249 pseudobonds, 81 residues, 3 models selected  

> select /A:2177

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 249 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084L_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A LEU 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> swapaa /A: 2084 arg

Using Dunbrack library  
/A LEU 2084: phi -131.8, psi 148.9 trans  
Applying ARG rotamer (chi angles: -64.2 -178.8 -179.3 -179.3) to /A ARG 2084  

> close #1.1-3

> select /A:2153

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> select /A:2153

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084R_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    6 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A ARG 2084 NH2  /A VAL 2057 CG1   0.633    2.887
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
6 clashes  

> select /A:2149-2150

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 6 pseudobonds, 81 residues, 2 models selected  

> select /A:2149-2151

22 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A:2093

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 6 pseudobonds, 81 residues, 2 models selected  

> select /A:2093

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 6 pseudobonds, 81 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084R_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    49 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A ARG 2084 NH2  /A VAL 2057 O    no hydrogen  2.820  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ARG 2084 O    no hydrogen  2.957  N/A
    

  
49 hydrogen bonds found  

> select /A:2238

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 55 pseudobonds, 81 residues, 3 models selected  

> select /A:2238

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 55 pseudobonds, 81 residues, 3 models selected  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084R_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    248 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A ARG 2084 NH2  /A VAL 2057 CG1   0.633    2.887
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2084 NH2  /A LEU 2058 CB    0.571    2.949
    /A ARG 2084 NE   /A VAL 2057 CG1   0.521    2.999
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A VAL 2081 CG1  /A ARG 2084 NE    0.437    3.083
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A ARG 2084 CD   /A VAL 2081 CG1   0.269    3.491
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A VAL 2081 CG1  /A ARG 2084 CZ    0.229    3.261
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A ARG 2084 CZ   /A VAL 2057 CG1   0.210    3.280
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A ARG 2084 CG   /A ALA 2082 O     0.148    3.152
    /A ARG 2084 NH2  /A VAL 2057 C     0.143    3.107
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A LEU 2058 CA   /A ARG 2084 NH2   0.045    3.475
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ARG 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ARG 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A LEU 2058 N    /A ARG 2084 NH2   -0.128    3.408
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A ARG 2084 CG   /A PRO 2083 O     -0.158    3.458
    /A VAL 2057 O    /A ARG 2084 NH2   -0.160    2.820
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A VAL 2081 CG1  /A ARG 2084 NH2   -0.177    3.697
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A ARG 2084 NH1  /A VAL 2081 CG1   -0.226    3.746
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A ARG 2084 CB   /A LEU 2041 O     -0.235    3.535
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A ARG 2084 NH2  /A VAL 2057 CB    -0.274    3.794
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ARG 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A ARG 2084 CZ   /A ILE 2025 CG2   -0.310    3.800
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ARG 2084 CG   /A VAL 2081 CG1   -0.355    4.115
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A VAL 2068 CG2  /A VAL 2073 CG2   -0.370    4.130
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
248 contacts  

> close #1.1-3

> select /A:2174

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> select /A:2174-2205

268 atoms, 273 bonds, 32 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

——— End of log from Wed Apr 30 15:52:46 2025 ———

> view name session-start

opened ChimeraX session  

> select add #1

18472 atoms, 18846 bonds, 2300 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

18472 atoms, 18846 bonds, 2300 residues, 1 model selected  

> hide sel atoms

> select subtract #1

Nothing selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> show sel atoms

> select subtract /A:2084

643 atoms, 653 bonds, 80 residues, 1 model selected  

> select /A:2115

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2114-2115

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> select /A:2084

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

> select /A:2084

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

> color sel orange

> swapaa /A: 2084 ile

Using Dunbrack library  
/A ARG 2084: phi -131.8, psi 148.9 trans  
Applying ILE rotamer (chi angles: 60.8 171.9) to /A ILE 2084  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> swapaa /A: 2068 ala

Using Dunbrack library  
Swapping /A VAL 2068 to ALA  

> color sel gray

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068A_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068A_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    238 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.375    3.385
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A ILE 2084 CD1  /A ILE 2086 CG1   0.332    3.428
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A ILE 2084 CG2  /A ALA 2082 O     0.252    3.048
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2084 CD1  /A LEU 2040 CD1   0.128    3.632
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.047    3.807
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.127    3.887
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2084 CG2  /A PRO 2083 O     -0.157    3.457
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A ILE 2084 CB   /A LEU 2041 O     -0.237    3.537
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A ILE 2086 CD1  /A ILE 2084 CG1   -0.249    4.009
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CG2  /A VAL 2081 CG1   -0.257    4.017
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A ALA 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
238 contacts  

> select /A:2270-2300

247 atoms, 249 bonds, 31 residues, 1 model selected  

> select /A:2270-2300

247 atoms, 249 bonds, 31 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068A_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A ALA 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A ALA 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

——— End of log from Fri May 2 10:11:43 2025 ———

> view name session-start

opened ChimeraX session  

> close #1.1-3

> select /A:2198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2198-2239

348 atoms, 356 bonds, 42 residues, 1 model selected  

> select /A:2198-2199

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2198-2238

343 atoms, 351 bonds, 41 residues, 1 model selected  

> color sel purple

> select add #1

18467 atoms, 18841 bonds, 2300 residues, 1 model selected  

> hide sel atoms

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2058,2081

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

> select /A:1977

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

> select /A:1977-2003

212 atoms, 214 bonds, 27 residues, 1 model selected  

> color sel cornflower blue

> select /A:1976

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1741-1976

1886 atoms, 1914 bonds, 236 residues, 1 model selected  

> hide sel cartoons

> select /A:1740

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1291-1740

3589 atoms, 3663 bonds, 450 residues, 1 model selected  

> hide sel cartoons

> select /A:1290

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

> select /A:963-1290

2634 atoms, 2702 bonds, 328 residues, 1 model selected  

> hide sel cartoons

> select /A:962

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:541-962

3403 atoms, 3476 bonds, 422 residues, 1 model selected  

> hide sel cartoons

> select /A:540

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:1-540

4362 atoms, 4446 bonds, 540 residues, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2004

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

> select /A:2004-2018

125 atoms, 127 bonds, 15 residues, 1 model selected  

> select /A:2239

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:2239-2300

490 atoms, 496 bonds, 62 residues, 1 model selected  

> hide sel cartoons

> select /A:2056

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

> select /A:2056-2102

377 atoms, 386 bonds, 47 residues, 1 model selected  

> color sel orange

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

——— End of log from Fri Jul 25 15:41:25 2025 ———

> view name session-start

opened ChimeraX session  

> ui windowfill toggle

> select clear

> ui mousemode right select

Drag select of 269 residues  

> cartoon style sel xsection oval modeHelix default

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> cartoon style sel xsection oval modeHelix default

> ui windowfill toggle

> select clear

> select /A:2208

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2208-2209

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> select /A:2208-2209

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2229-2230

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2229-2233

41 atoms, 40 bonds, 5 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A ALA 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A ALA 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> select /A:2244

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2244-2245

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> select /A:2180

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

> select /A:2180-2188

72 atoms, 73 bonds, 9 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028

73 atoms, 72 bonds, 9 residues, 1 model selected  

> select /A:1977-1978

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1977-1980

34 atoms, 34 bonds, 4 residues, 1 model selected  

> select /A:1977

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

> select /A:1977-1994

153 atoms, 155 bonds, 18 residues, 1 model selected  

> select /A:1977

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

> select /A:1977-2003

212 atoms, 214 bonds, 27 residues, 1 model selected  

> ui windowfill toggle

> select /A:2059

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

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel black

> color sel lime

> select clear

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOut.tif width 1280 height 491
> supersample 3

Drag select of 67 atoms, 262 residues, 54 bonds  

> show sel surfaces

> transparency (#!1 & sel) 70

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOutSurface.tif width 1280 height
> 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
303175 of 2695328 triangles, 67 atoms, 262 residues, 54 bonds  

> hide sel surfaces

> ui windowfill toggle

> select clear

> ui windowfill toggle

> select clear

[Repeated 1 time(s)]

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) orange

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add /A:2056

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add /A:2058

26 atoms, 23 bonds, 3 residues, 2 models selected  

> select add /A:2059

37 atoms, 33 bonds, 4 residues, 2 models selected  

> select add /A:2060

45 atoms, 40 bonds, 5 residues, 2 models selected  

> select add /A:2079

53 atoms, 47 bonds, 6 residues, 2 models selected  

> select add /A:2080

61 atoms, 54 bonds, 7 residues, 2 models selected  

> select add /A:2081

68 atoms, 60 bonds, 8 residues, 2 models selected  
Drag select of 67 atoms, 262 residues, 54 bonds  

> hide sel atoms

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) orange

> color (#!1 & sel) red

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOut.tif width 1280 height 491
> supersample 3

Drag select of 262 residues  

> show sel surfaces

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOutSurface.tif width 1280 height
> 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
301155 of 2695328 triangles, 262 residues  

> hide sel surfaces

> select clear

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) orange red

> color (#!1 & sel) orange

> select clear

> select /A:2056

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

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add /A:2056

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add /A:2058

26 atoms, 23 bonds, 3 residues, 2 models selected  

> select add /A:2059

37 atoms, 33 bonds, 4 residues, 2 models selected  

> select add /A:2060

45 atoms, 40 bonds, 5 residues, 2 models selected  

> select add /A:2079

53 atoms, 47 bonds, 6 residues, 2 models selected  

> select add /A:2080

61 atoms, 54 bonds, 7 residues, 2 models selected  

> select add /A:2081

68 atoms, 60 bonds, 8 residues, 2 models selected  

> select add /A:2082

73 atoms, 64 bonds, 9 residues, 2 models selected  

> select add /A:2083

80 atoms, 71 bonds, 10 residues, 2 models selected  

> select add /A:2020

88 atoms, 78 bonds, 11 residues, 2 models selected  

> select add /A:2021

97 atoms, 86 bonds, 12 residues, 2 models selected  

> select add /A:2022

105 atoms, 93 bonds, 13 residues, 2 models selected  

> select add /A:2023

109 atoms, 96 bonds, 14 residues, 2 models selected  

> select add /A:2042

114 atoms, 100 bonds, 15 residues, 2 models selected  

> select add /A:2041

122 atoms, 107 bonds, 16 residues, 2 models selected  

> select add /A:2084

130 atoms, 114 bonds, 17 residues, 2 models selected  

> select add /A:2085

137 atoms, 120 bonds, 18 residues, 2 models selected  

> select add /A:2024

145 atoms, 127 bonds, 19 residues, 2 models selected  

> select add /A:2025

153 atoms, 134 bonds, 20 residues, 2 models selected  

> select add /A:2026

164 atoms, 144 bonds, 21 residues, 2 models selected  

> ui windowfill toggle

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    1 clashes
         atom1           atom2       overlap  distance
    /A ARG 2056 NH1  /A GLU 2021 CD   0.731    2.789
    

  
1 clashes  

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> select add #1.2

164 atoms, 161 bonds, 1 pseudobond, 21 residues, 3 models selected  

> select subtract #1.2

164 atoms, 161 bonds, 21 residues, 2 models selected  

> show #1.1 models

> select subtract #1.1

1 model selected  

> select add #1.1

18467 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> close #1.1-2

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select subtract /A:2021

155 atoms, 151 bonds, 20 residues, 1 model selected  

> select subtract /A:2022

147 atoms, 143 bonds, 19 residues, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select clear

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2057-2058

15 atoms, 14 bonds, 2 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2057-2058

15 atoms, 14 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select subtract /A:2056

153 atoms, 150 bonds, 20 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    51 contacts
         atom1            atom2       overlap  distance
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A ALA 2082 O    /A ILE 2084 CG2   0.252    3.048
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A PRO 2083 O    /A ILE 2084 CG2   -0.157    3.457
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A ILE 2084 CB   /A LEU 2041 O     -0.237    3.537
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CG2  /A VAL 2081 CG1   -0.257    4.017
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    

  
51 contacts  

> hide sel cartoons

> select clear

> ui windowfill toggle

> select clear

> ui mousemode right translate

> ui windowfill toggle

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select subtract /A:2056

153 atoms, 150 bonds, 51 pseudobonds, 20 residues, 2 models selected  

> style sel ball

Changed 153 atom styles  

> style sel stick

Changed 153 atom styles  

> ui windowfill toggle

> select clear

> save C:/Users/emirm/Desktop/contacts/l2058_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select subtract /A:2056

153 atoms, 150 bonds, 51 pseudobonds, 20 residues, 2 models selected  

> hide #1.3 models

> hide #1.2 models

> show #1.3 models

> hide #1.3 models

> close #1.3

> hide #1.1 models

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    10 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N  /A ILE 2060 O  no hydrogen  2.857  N/A
    /A LEU 2022 N  /A LEU 2058 O  no hydrogen  2.913  N/A
    /A LEU 2041 N  /A THR 2085 O  no hydrogen  3.063  N/A
    /A VAL 2057 N  /A LEU 2022 O  no hydrogen  2.815  N/A
    /A LEU 2058 N  /A LEU 2022 O  no hydrogen  3.346  N/A
    /A ARG 2059 N  /A ASN 2080 O  no hydrogen  2.872  N/A
    /A ILE 2060 N  /A LEU 2020 O  no hydrogen  2.817  N/A
    /A ASN 2080 N  /A ARG 2059 O  no hydrogen  2.752  N/A
    /A ALA 2082 N  /A VAL 2057 O  no hydrogen  2.859  N/A
    /A THR 2085 N  /A LEU 2041 O  no hydrogen  2.749  N/A
    

  
10 hydrogen bonds found  

> ui windowfill toggle

> select clear

> save C:/Users/emirm/Desktop/contacts/l2058_hb.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.3 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> swapaa /A: 2058 pro

Using Dunbrack library  
/A LEU 2058: phi -137.9, psi 132.6 trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /A PRO 2058  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

163 atoms, 161 bonds, 53 pseudobonds, 21 residues, 3 models selected  

> select subtract /A:2056

152 atoms, 150 bonds, 53 pseudobonds, 20 residues, 3 models selected  

> ui windowfill toggle

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    1 clashes
        atom1            atom2       overlap  distance
    /A PRO 2058 CD  /A VAL 2057 CG1   0.963    2.797
    

  
1 clashes  

> ui windowfill toggle

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select subtract #1.2

152 atoms, 150 bonds, 10 pseudobonds, 20 residues, 2 models selected  

> select subtract #1.3

152 atoms, 150 bonds, 20 residues, 1 model selected  

> close #1.2-3

> ui windowfill toggle

> ui tool show Clashes

> color bfactor sel

152 atoms, 20 residues, atom bfactor range 49.1 to 89.1  

> undo

> ui tool show Clashes

> ui windowfill toggle

> close #1.1

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

152 atoms, 150 bonds, 20 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

163 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2057-2058

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

152 atoms, 150 bonds, 20 residues, 1 model selected  

> ui tool show "Add Hydrogens"

> addh

Summary of feedback from adding hydrogens to
fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
notes | Termini for fold_2025_02_26_14_57_hob_native_model_0.cif (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 2300  
Chain-final residues that are not actual C termini:  
1901 hydrogen bonds  
18569 hydrogens added  
  

> ui windowfill toggle

> ui tool show "Color Actions"

> ui windowfill toggle

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    1 clashes
        atom1            atom2       overlap  distance
    /A PRO 2058 CD  /A VAL 2057 CG1   0.603    2.797
    

  
1 clashes  

> ui windowfill toggle

[Repeated 1 time(s)]

> color bfactor sel

152 atoms, 20 residues, atom bfactor range 49.1 to 89.1  

> undo

> style sel ball

Changed 152 atom styles  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    30 contacts
         atom1            atom2       overlap  distance
    /A VAL 2057 CG1  /A PRO 2058 CD    0.603    2.797
    /A VAL 2057 CG2  /A GLY 2023 O     0.249    2.871
    /A ILE 2084 CG2  /A ALA 2082 O     0.072    3.048
    /A LEU 2041 CD2  /A ARG 2026 CG    0.064    3.336
    /A THR 2085 N    /A LEU 2041 O     -0.104    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.107    2.752
    /A PRO 2058 CG   /A VAL 2057 CG1   -0.112    3.512
    /A VAL 2057 CG1  /A ILE 2025 CG2   -0.121    3.521
    /A ARG 2059 CA   /A LEU 2020 O     -0.146    3.266
    /A ILE 2084 CA   /A LEU 2041 O     -0.164    3.284
    /A VAL 2057 N    /A LEU 2022 O     -0.170    2.815
    /A ILE 2060 N    /A LEU 2020 O     -0.172    2.817
    /A ILE 2060 O    /A LEU 2020 N     -0.212    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.214    2.859
    /A ARG 2059 N    /A ASN 2080 O     -0.227    2.872
    /A ILE 2025 N    /A ASN 2024 OD1   -0.233    2.878
    /A GLU 2021 N    /A LEU 2020 CD2   -0.254    3.579
    /A ARG 2026 CD   /A LEU 2041 CD2   -0.255    3.655
    /A LEU 2022 N    /A PRO 2058 O     -0.268    2.913
    /A ALA 2082 O    /A VAL 2081 CG1   -0.274    3.394
    /A PRO 2058 CD   /A LEU 2022 O     -0.283    3.403
    /A PRO 2058 N    /A LEU 2022 O     -0.286    3.346
    /A VAL 2081 CA   /A VAL 2057 O     -0.336    3.456
    /A PRO 2083 O    /A ILE 2084 CG2   -0.337    3.457
    /A PRO 2058 O    /A GLU 2021 CA    -0.342    3.462
    /A ASN 2080 O    /A PRO 2058 CA    -0.344    3.464
    /A PRO 2058 CG   /A VAL 2057 CB    -0.369    3.769
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.369    3.769
    /A LEU 2022 CB   /A PRO 2058 CD    -0.391    3.791
    /A GLU 2021 CG   /A LEU 2020 O     -0.393    3.513
    

  
30 contacts  

> ui windowfill toggle

[Repeated 1 time(s)]

> style sel stick

Changed 43 atom styles  

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2085

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 30 pseudobonds, 20 residues, 2 models selected  

> select /A:2079-2085

106 atoms, 106 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 30 pseudobonds, 20 residues, 2 models selected  

> style sel stick

Changed 325 atom styles  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> ui windowfill toggle

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    130 contacts
         atom1             atom2        overlap  distance
    /A PRO 2058 HD2   /A VAL 2057 CB     1.082    1.618
    /A PRO 2058 HD2   /A VAL 2057 CG1    0.984    1.716
    /A VAL 2057 HB    /A PRO 2058 CD     0.618    2.082
    /A VAL 2057 CG1   /A PRO 2058 CD     0.603    2.797
    /A VAL 2057 HB    /A PRO 2058 HD2    0.482    1.518
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A PRO 2058 HD2   /A VAL 2057 HG13   0.201    1.799
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A PRO 2058 HD2   /A VAL 2057 HG12   0.194    1.806
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2022 HD21  /A PRO 2058 HG3    0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HB3   /A PRO 2058 HD3    0.025    1.975
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A VAL 2057 HB    /A PRO 2058 HD3    0.015    1.985
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A VAL 2057 HG13  /A PRO 2058 CD     -0.013    2.713
    /A VAL 2057 HG12  /A PRO 2058 CD     -0.013    2.713
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A LEU 2022 HB3   /A PRO 2058 CD     -0.097    2.797
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A PRO 2058 CG    /A VAL 2057 CG1    -0.112    3.512
    /A VAL 2057 CB    /A PRO 2058 HD3    -0.115    2.815
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2022 HD21  /A PRO 2058 CG     -0.135    2.835
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A LEU 2022 CB    /A PRO 2058 HD3    -0.144    2.844
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A PRO 2058 HD3   /A LEU 2022 O      -0.277    2.697
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A PRO 2058 CD    /A LEU 2022 O      -0.283    3.403
    /A PRO 2058 N     /A LEU 2022 O      -0.286    3.346
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 HG3   /A LEU 2022 CD2    -0.297    2.997
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A PRO 2058 HB2   /A LEU 2022 HB3    -0.354    2.354
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.357    3.057
    /A LEU 2022 HB3   /A PRO 2058 CB     -0.361    3.061
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A PRO 2058 CG    /A VAL 2057 CB     -0.369    3.769
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A LEU 2022 CB    /A PRO 2058 CD     -0.391    3.791
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A PRO 2058 HG2   /A VAL 2057 O      -0.393    2.813
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.400    3.100
    

  
130 contacts  

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> ui windowfill toggle

[Repeated 2 time(s)]

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select add #1.1

146 atoms, 130 pseudobonds, 20 residues, 2 models selected  

> select subtract #1.1

146 atoms, 20 residues, 1 model selected  

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058p_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.1 models

> show #1.1 models

> show #1.2 models

> hide #1.1 models

> ui windowfill toggle

> select add /A:2022@CG

1 atom, 1 residue, 1 model selected  

> select subtract /A:2022@CG

Nothing selected  

> select add /A:2022@CA

1 atom, 1 residue, 1 model selected  

> ui windowfill toggle

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 134 pseudobonds, 20 residues, 3 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> hide sel atoms

> show sel atoms

> show sel cartoons

> hide sel atoms

> show sel atoms

> hide sel cartoons

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058p_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 134 pseudobonds, 20 residues, 3 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

> show sel atoms

> hide sel atoms

> show sel cartoons

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058p_cla2.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.2 models

> hide #!1 models

> show #!1 models

> show #1.1 models

> select add #1.1

130 pseudobonds, 1 model selected  

> select subtract #1.1

Nothing selected  

> select add #1.1

130 pseudobonds, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true

Atom specifier selects no atoms  

> select subtract #1.1

Nothing selected  

> hide #1.1 models

> show #1.1 models

> select add #1

37035 atoms, 37410 bonds, 134 pseudobonds, 2300 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 134 pseudobonds, 20 residues, 3 models selected  

> ui tool show Contacts

> close #1.1-2

> ui tool show Contacts

Restriction atom specifier must not be blank  

> ui tool show Contacts

> contacts sel intraRes true ignoreHiddenModels true select true color #ffffff
> dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    323 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 CB    /A PRO 2058 HD2    1.082    1.618
    /A VAL 2057 CG1   /A PRO 2058 HD2    0.984    1.716
    /A GLU 2021 CD    /A ARG 2056 NH1    0.716    2.789
    /A PRO 2083 HB3   /A ILE 2045 HD12   0.629    1.371
    /A PRO 2058 CD    /A VAL 2057 HB     0.618    2.082
    /A PRO 2058 CD    /A VAL 2057 CG1    0.603    2.797
    /A THR 2085 HG1   /A THR 2043 OG1    0.505    1.595
    /A GLU 2021 CD    /A ARG 2056 CZ     0.496    2.994
    /A PRO 2058 HD2   /A VAL 2057 HB     0.482    1.518
    /A GLU 2021 OE2   /A ARG 2056 CZ     0.469    2.561
    /A ALA 2082 O     /A ILE 2084 HG22   0.435    1.985
    /A GLU 2021 OE1   /A ARG 2056 NH1    0.430    2.215
    /A ASN 2080 OD1   /A PRO 2182 HG2    0.403    2.017
    /A PRO 2083 HB3   /A ILE 2045 CD1    0.352    2.348
    /A VAL 2057 HG23  /A ASN 2024 HA     0.336    1.664
    /A VAL 2057 HG12  /A ILE 2025 HG21   0.327    1.673
    /A ASN 2024 HB3   /A SER 2002 OG     0.311    2.189
    /A PRO 2083 CB    /A ILE 2045 HD12   0.299    2.401
    /A LEU 2041 CD2   /A ARG 2026 HG3    0.297    2.403
    /A THR 2085 HG1   /A THR 2043 CB     0.286    2.414
    /A ASN 2080 HD22  /A GLU 2078 CD     0.273    2.607
    /A ASN 2080 H     /A ARG 2059 O      0.258    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.249    2.871
    /A THR 2085 H     /A LEU 2041 O      0.230    1.790
    /A ARG 2026 O     /A VAL 2000 H      0.204    1.816
    /A VAL 2057 HG13  /A PRO 2058 HD2    0.201    1.799
    /A ILE 2060 H     /A LEU 2020 O      0.195    1.825
    /A VAL 2057 HG12  /A PRO 2058 HD2    0.194    1.806
    /A ILE 2025 CG2   /A VAL 2057 HG12   0.191    2.509
    /A ARG 2026 HA    /A LEU 2040 O      0.189    2.231
    /A GLU 2021 H     /A LEU 2005 O      0.173    1.847
    /A ILE 2060 O     /A LEU 2020 H      0.170    1.850
    /A ALA 2082 H     /A VAL 2057 O      0.168    1.852
    /A VAL 2057 O     /A VAL 2057 HG13   0.156    2.264
    /A ILE 2084 HG21  /A ILE 2084 HD11   0.156    1.844
    /A ASN 2080 O     /A ARG 2059 H      0.148    1.872
    /A ASN 2024 CB    /A SER 2002 OG     0.136    3.064
    /A LEU 2020 O     /A ARG 2059 HA     0.122    2.298
    /A ARG 2059 HE    /A LEU 2019 HD13   0.121    1.879
    /A ILE 2079 O     /A PRO 2182 HD3    0.120    2.300
    /A ARG 2026 NH2   /A GLU 2028 OE1    0.119    2.526
    /A ALA 2082 O     /A VAL 2081 HG11   0.113    2.307
    /A PRO 2083 HB2   /A THR 2043 O      0.108    2.312
    /A LEU 2020 C     /A LEU 2020 HD21   0.098    2.512
    /A ASN 2080 OD1   /A PRO 2182 CG     0.098    3.022
    /A LEU 2041 HD13  /A ASP 2038 CG     0.096    2.784
    /A ILE 2079 HD11  /A PHE 2077 CE1    0.091    2.609
    /A ILE 2084 O     /A ILE 2084 HG13   0.085    2.335
    /A PRO 2083 CB    /A ILE 2045 CD1    0.084    3.316
    /A GLU 2021 OE1   /A ARG 2056 CZ     0.084    2.946
    /A THR 2085 H     /A THR 2043 HG1    0.084    1.916
    /A VAL 2057 CG1   /A ILE 2025 HG21   0.083    2.617
    /A PRO 2083 HA    /A PRO 2185 O      0.076    2.344
    /A ALA 2082 O     /A ILE 2084 CG2    0.072    3.048
    /A ARG 2026 CG    /A LEU 2041 CD2    0.064    3.336
    /A THR 2085 OG1   /A THR 2043 OG1    0.058    2.542
    /A ILE 2060 HA    /A GLU 2078 O      0.053    2.367
    /A PRO 2058 HG3   /A LEU 2022 HD21   0.053    1.947
    /A GLU 2021 CD    /A ARG 2056 NE     0.052    3.453
    /A THR 2085 HA    /A ARG 2187 O      0.051    2.369
    /A ARG 2059 HD2   /A ARG 2059 HH11   0.047    1.953
    /A ILE 2084 O     /A ARG 2187 H      0.043    1.977
    /A THR 2085 HG1   /A THR 2043 CG2    0.042    2.658
    /A THR 2085 CB    /A THR 2043 OG1    0.038    3.162
    /A ILE 2084 HD12  /A ILE 2086 CG1    0.027    2.673
    /A THR 2085 O     /A LEU 2040 HA     0.026    2.394
    /A PRO 2058 HD3   /A LEU 2022 HB3    0.025    1.975
    /A PRO 2083 O     /A THR 2043 H      0.023    1.997
    /A ARG 2026 CZ    /A GLU 2028 OE1    0.021    3.009
    /A PRO 2058 O     /A LEU 2022 H      0.018    2.002
    /A ILE 2084 CD1   /A ILE 2086 CD1    0.015    3.385
    /A PRO 2058 HD3   /A VAL 2057 HB     0.015    1.985
    /A LEU 2041 HD23  /A ARG 2026 HG3    0.013    1.987
    /A ILE 2079 HD11  /A PHE 2077 HE1    0.013    1.987
    /A LEU 2041 HD22  /A ARG 2026 HG3    0.013    1.987
    /A ASN 2080 ND2   /A GLU 2078 CD     0.011    3.494
    /A THR 2085 N     /A THR 2043 HG1    0.011    2.614
    /A GLU 2021 CD    /A ARG 2056 NH2    0.010    3.495
    /A ARG 2059 HE    /A LEU 2019 CD1    0.010    2.690
    /A ILE 2084 HD12  /A LEU 2040 CD1    0.009    2.691
    /A GLU 2021 O     /A LEU 2005 H      0.008    2.012
    /A LEU 2041 CD1   /A ASP 2038 HB3    0.006    2.694
    /A LEU 2041 HD13  /A ASP 2038 CB     -0.001    2.701
    /A ASN 2080 HD22  /A GLU 2078 OE1    -0.004    2.024
    /A ASN 2080 HB3   /A ARG 2059 HB3    -0.009    2.009
    /A PRO 2058 CD    /A VAL 2057 HG13   -0.013    2.713
    /A PRO 2058 CD    /A VAL 2057 HG12   -0.013    2.713
    /A VAL 2057 CG2   /A ASN 2024 HA     -0.023    2.723
    /A ARG 2026 H     /A VAL 2000 O      -0.023    2.043
    /A LEU 2022 CD2   /A ILE 2025 HB     -0.023    2.723
    /A THR 2085 OG1   /A ARG 2187 HB3    -0.027    2.527
    /A ILE 2084 CD1   /A ILE 2086 CG1    -0.028    3.428
    /A ILE 2079 HG21  /A ILE 2079 HD13   -0.029    2.029
    /A ILE 2084 HD12  /A LEU 2040 HD12   -0.031    2.031
    /A ILE 2025 HG23  /A ILE 2025 HD13   -0.032    2.032
    /A VAL 2057 HG23  /A ASN 2024 CA     -0.037    2.737
    /A LEU 2022 O     /A VAL 2057 H      -0.039    2.059
    /A ILE 2079 O     /A PRO 2182 CD     -0.040    3.160
    /A GLY 2023 O     /A VAL 2057 HG23   -0.045    2.465
    /A GLY 2023 O     /A VAL 2057 HG22   -0.046    2.466
    /A ILE 2025 HB    /A LEU 2022 HD22   -0.047    2.047
    /A ILE 2084 O     /A VAL 2186 HA     -0.047    2.467
    /A ARG 2026 O     /A LEU 1999 HD11   -0.059    2.479
    /A GLY 2023 HA3   /A ALA 2003 HB2    -0.061    2.061
    /A GLU 2021 OE2   /A ARG 2056 NH2    -0.061    2.706
    /A LEU 2022 HD13  /A LEU 2001 HB3    -0.066    2.066
    /A LEU 2041 HD13  /A ASP 2038 HB3    -0.066    2.066
    /A ILE 2079 H     /A LYS 2180 O      -0.068    2.088
    /A ILE 2025 CD1   /A LEU 2040 CD2    -0.069    3.469
    /A ILE 2060 HG21  /A ILE 2060 HD13   -0.076    2.076
    /A GLU 2021 CD    /A ARG 2056 HH11   -0.077    2.957
    /A ARG 2026 HH21  /A GLU 2028 OE1    -0.078    2.098
    /A THR 2085 O     /A LEU 2041 H      -0.080    2.100
    /A ARG 2026 O     /A LEU 1999 HA     -0.082    2.502
    /A ILE 2025 CD1   /A LEU 2040 HD21   -0.085    2.785
    /A ILE 2084 CD1   /A LEU 2040 HD12   -0.085    2.785
    /A ILE 2060 O     /A LEU 2019 HA     -0.089    2.509
    /A ALA 2082 CB    /A VAL 2057 HA     -0.091    2.791
    /A PRO 2058 O     /A GLU 2021 HA     -0.095    2.515
    /A ILE 2025 HA    /A VAL 2000 O      -0.096    2.516
    /A PRO 2058 CD    /A LEU 2022 HB3    -0.097    2.797
    /A LEU 2020 HD21  /A GLU 2021 N      -0.097    2.722
    /A LEU 2020 HB3   /A ILE 2060 HB     -0.100    2.100
    /A ARG 2026 CA    /A LEU 2040 O      -0.102    3.222
    /A ILE 2079 O     /A ILE 2181 HG22   -0.102    2.522
    /A VAL 2081 HB    /A VAL 2184 HG22   -0.103    2.103
    /A LEU 2041 O     /A THR 2085 N      -0.104    2.749
    /A VAL 2057 O     /A VAL 2081 HA     -0.105    2.525
    /A ILE 2079 CD1   /A PHE 2077 CE1    -0.105    3.505
    /A ASN 2080 O     /A PRO 2058 HA     -0.106    2.526
    /A LEU 2041 O     /A ILE 2084 HA     -0.106    2.526
    /A ARG 2059 O     /A ASN 2080 N      -0.107    2.752
    /A ALA 2042 C     /A THR 2043 HG1    -0.108    2.718
    /A VAL 2057 CG1   /A PRO 2058 CG     -0.112    3.512
    /A LEU 2041 CD1   /A ASP 2038 CB     -0.113    3.513
    /A PRO 2058 HD3   /A VAL 2057 CB     -0.115    2.815
    /A ILE 2025 O     /A ILE 2025 HG22   -0.117    2.537
    /A ILE 2025 CG2   /A VAL 2057 CG1    -0.121    3.521
    /A PRO 2083 CD    /A ALA 2082 HB1    -0.122    2.822
    /A THR 2085 OG1   /A THR 2043 CB     -0.122    3.322
    /A THR 2085 OG1   /A THR 2043 HG21   -0.134    2.634
    /A PRO 2058 CG    /A LEU 2022 HD21   -0.135    2.835
    /A LEU 2022 CD2   /A LEU 2001 HD23   -0.135    2.835
    /A ARG 2026 CG    /A LEU 2041 HD22   -0.139    2.839
    /A GLU 2021 O     /A PHE 2004 HA     -0.139    2.559
    /A GLU 2021 CD    /A ARG 2056 CD     -0.141    3.721
    /A LEU 2041 HG    /A LEU 2040 C      -0.142    2.752
    /A ALA 2082 HA    /A PRO 2083 HD2    -0.144    2.144
    /A PRO 2058 HD3   /A LEU 2022 CB     -0.144    2.844
    /A LEU 2020 O     /A ARG 2059 CA     -0.146    3.266
    /A LEU 2022 HD22  /A LEU 2001 HD23   -0.148    2.148
    /A THR 2085 HG1   /A THR 2043 HG1    -0.151    2.151
    /A THR 2085 OG1   /A THR 2043 CG2    -0.155    3.355
    /A VAL 2057 HA    /A ALA 2082 HB2    -0.156    2.156
    /A VAL 2081 HG21  /A ILE 2079 HG23   -0.159    2.159
    /A ILE 2079 HB    /A ILE 2181 HG13   -0.159    2.159
    /A GLU 2021 CD    /A ARG 2056 HH12   -0.159    3.039
    /A PRO 2083 HB3   /A ILE 2045 CG1    -0.161    2.861
    /A ALA 2082 N     /A VAL 2081 HG11   -0.163    2.788
    /A GLY 2023 H     /A SER 2002 O      -0.163    2.183
    /A LEU 2041 O     /A ILE 2084 CA     -0.164    3.284
    /A ARG 2026 O     /A VAL 2000 N      -0.169    2.814
    /A ARG 2026 CG    /A LEU 2041 HD23   -0.169    2.869
    /A LEU 2022 O     /A VAL 2057 N      -0.170    2.815
    /A LEU 2020 O     /A ILE 2060 N      -0.172    2.817
    /A LEU 2020 HA    /A LEU 2005 O      -0.173    2.593
    /A THR 2085 CA    /A ARG 2187 O      -0.173    3.293
    /A LEU 2022 HA    /A LEU 2022 HD11   -0.175    2.175
    /A ILE 2084 HG22  /A PRO 2083 C      -0.176    2.786
    /A GLU 2021 CD    /A ARG 2056 HD3    -0.176    3.056
    /A ILE 2025 H     /A ASN 2024 OD1    -0.178    2.198
    /A ASN 2024 HB3   /A SER 2002 HG     -0.178    2.178
    /A VAL 2081 CG2   /A ILE 2079 HG23   -0.180    2.880
    /A GLU 2021 HB3   /A ARG 2056 HD3    -0.183    2.183
    /A ASN 2024 O     /A SER 2002 H      -0.184    2.204
    /A PRO 2083 CA    /A PRO 2185 O      -0.184    3.304
    /A GLU 2021 N     /A LEU 2005 O      -0.185    2.830
    /A ILE 2060 HG12  /A ILE 2079 HG22   -0.190    2.190
    /A LEU 2020 HD12  /A PHE 2004 HE2    -0.192    2.192
    /A THR 2085 HG1   /A THR 2043 HG21   -0.194    2.194
    /A ILE 2084 HD12  /A ILE 2086 HG12   -0.197    2.197
    /A GLU 2021 OE1   /A ARG 2056 HH12   -0.197    2.217
    /A ILE 2079 CD1   /A PHE 2077 HE1    -0.200    2.900
    /A LEU 2022 CD1   /A LEU 2001 HB3    -0.200    2.900
    /A ILE 2060 CA    /A GLU 2078 O      -0.201    3.321
    /A ILE 2084 CG1   /A VAL 2186 HG11   -0.202    2.902
    /A LEU 2041 HD22  /A LEU 2041 HA     -0.205    2.205
    /A ILE 2025 HG13  /A LEU 2040 HD21   -0.206    2.206
    /A ASN 2024 O     /A LEU 2001 HA     -0.208    2.628
    /A LEU 2020 N     /A ILE 2060 O      -0.212    2.857
    /A VAL 2057 O     /A ALA 2082 N      -0.214    2.859
    /A VAL 2081 HB    /A VAL 2184 CG2    -0.222    2.922
    /A ARG 2026 NH2   /A GLU 2028 CD     -0.223    3.728
    /A ILE 2025 HG12  /A LEU 2001 CD2    -0.223    2.923
    /A GLU 2021 OE2   /A ARG 2056 NH1    -0.226    2.871
    /A ASN 2080 O     /A ARG 2059 N      -0.227    2.872
    /A ILE 2025 CG1   /A LEU 2040 HD21   -0.229    2.929
    /A LEU 2022 HD22  /A LEU 2001 CD2    -0.231    2.931
    /A LEU 2020 HB2   /A TYR 2006 HD2    -0.232    2.232
    /A ILE 2084 CD1   /A LEU 2040 CD1    -0.232    3.632
    /A ASN 2024 OD1   /A ILE 2025 N      -0.233    2.878
    /A GLU 2021 OE1   /A LEU 2019 HD23   -0.237    2.657
    /A ILE 2079 HD11  /A PHE 2077 CZ     -0.239    2.939
    /A ILE 2079 O     /A ILE 2181 HA     -0.241    2.661
    /A ILE 2025 HG12  /A LEU 2001 HD21   -0.241    2.241
    /A ARG 2059 NE    /A LEU 2019 HD13   -0.243    2.868
    /A GLU 2021 HG3   /A LEU 2019 HG     -0.243    2.243
    /A ILE 2084 O     /A VAL 2186 CA     -0.246    3.366
    /A LEU 2041 HG    /A LEU 2040 O      -0.249    2.669
    /A ILE 2084 HD13  /A ILE 2086 CD1    -0.250    2.950
    /A ALA 2082 HB1   /A PRO 2083 HD3    -0.251    2.251
    /A ILE 2084 HD12  /A ILE 2086 CD1    -0.251    2.951
    /A ARG 2059 O     /A ILE 2079 HA     -0.253    2.673
    /A LEU 2020 CD2   /A GLU 2021 N      -0.254    3.579
    /A LEU 2041 CD2   /A ARG 2026 CD     -0.255    3.655
    /A ARG 2026 HH21  /A GLU 2028 CD     -0.261    3.141
    /A ILE 2084 HG13  /A ILE 2086 HG13   -0.261    2.261
    /A LEU 2041 CD1   /A ASP 2038 CG     -0.261    3.841
    /A LEU 2041 CG    /A LEU 2040 O      -0.262    3.382
    /A THR 2085 O     /A LEU 2040 CA     -0.262    3.382
    /A GLU 2021 HG2   /A ARG 2059 HG3    -0.264    2.264
    /A PRO 2083 CB    /A THR 2043 O      -0.268    3.388
    /A PRO 2058 O     /A LEU 2022 N      -0.268    2.913
    /A ILE 2025 CG1   /A LEU 1999 HD13   -0.269    2.969
    /A ASN 2024 CG    /A ILE 2025 H      -0.272    2.882
    /A GLU 2021 CD    /A LEU 2019 HD23   -0.273    3.153
    /A GLY 2023 CA    /A SER 2002 O      -0.273    3.393
    /A LEU 2022 HD13  /A LEU 2001 CB     -0.274    2.974
    /A VAL 2081 CG1   /A ALA 2082 O      -0.274    3.394
    /A LEU 2022 O     /A PRO 2058 HD3    -0.277    2.697
    /A ARG 2026 HD3   /A ARG 2026 HH11   -0.280    2.280
    /A PRO 2083 CB    /A ILE 2045 CG1    -0.282    3.682
    /A LEU 2022 O     /A PRO 2058 CD     -0.283    3.403
    /A GLU 2021 OE1   /A ARG 2056 HH11   -0.284    2.304
    /A VAL 2081 O     /A VAL 2184 HG23   -0.284    2.704
    /A LEU 2022 O     /A PRO 2058 N      -0.286    3.346
    /A LEU 2022 HD12  /A PHE 2004 HD2    -0.289    2.289
    /A PRO 2083 CG    /A ILE 2045 HD12   -0.289    2.989
    /A ARG 2026 HB3   /A VAL 2000 HB     -0.290    2.290
    /A THR 2085 HG23  /A ILE 2086 N      -0.291    2.916
    /A LEU 2020 C     /A GLU 2021 HG3    -0.291    2.901
    /A ASN 2080 ND2   /A GLU 2078 HG3    -0.292    2.917
    /A ILE 2084 HG12  /A VAL 2186 HG11   -0.292    2.292
    /A LEU 2022 CD2   /A PRO 2058 HG3    -0.297    2.997
    /A ILE 2079 N     /A GLU 2078 HG3    -0.298    2.923
    /A THR 2085 HA    /A ARG 2187 HB3    -0.302    2.302
    /A VAL 2057 C     /A ALA 2082 H      -0.307    2.917
    /A ASN 2024 CB    /A SER 2002 HG     -0.308    3.008
    /A LEU 2020 HD21  /A LEU 2020 O      -0.308    2.728
    /A ARG 2026 O     /A LEU 1999 CA     -0.309    3.429
    /A LEU 2041 O     /A THR 2043 HG1    -0.310    2.330
    /A ILE 2025 CD1   /A LEU 1999 HD13   -0.311    3.011
    /A ILE 2084 O     /A ARG 2187 N      -0.312    2.957
    /A ASN 2080 ND2   /A GLU 2078 OE1    -0.313    2.958
    /A GLY 2023 N     /A SER 2002 O      -0.315    2.960
    /A LEU 2041 HD23  /A ARG 2026 CD     -0.316    3.016
    /A LEU 2020 CD1   /A PHE 2004 HE2    -0.318    3.018
    /A ILE 2060 HG23  /A PHE 2061 N      -0.321    2.946
    /A VAL 2081 O     /A VAL 2184 HG13   -0.322    2.742
    /A ARG 2026 HG2   /A MET 2027 N      -0.325    2.950
    /A ILE 2060 O     /A LEU 2019 CA     -0.325    3.445
    /A GLY 2023 CA    /A ALA 2003 HB2    -0.326    3.026
    /A PRO 2083 CB    /A ILE 2045 HG13   -0.326    3.026
    /A THR 2085 OG1   /A ARG 2187 CB     -0.327    3.527
    /A ASN 2080 C     /A VAL 2081 HG21   -0.327    2.937
    /A PRO 2083 CG    /A ILE 2045 CD1    -0.330    3.730
    /A ASN 2024 H     /A SER 2002 O      -0.334    2.354
    /A VAL 2057 O     /A VAL 2081 CA     -0.336    3.456
    /A ILE 2084 CG2   /A PRO 2083 O      -0.337    3.457
    /A ILE 2079 CG1   /A PHE 2077 CE1    -0.339    3.739
    /A GLU 2021 CA    /A PRO 2058 O      -0.342    3.462
    /A ARG 2059 NE    /A LEU 2019 CD1    -0.342    3.667
    /A LEU 2041 HD23  /A ARG 2026 NE     -0.343    2.968
    /A PRO 2058 CA    /A ASN 2080 O      -0.344    3.464
    /A LEU 2020 C     /A ILE 2060 H      -0.344    2.954
    /A ARG 2026 N     /A ILE 2025 HG13   -0.346    2.971
    /A ALA 2042 CB    /A VAL 2057 HG21   -0.353    3.053
    /A LEU 2022 HD11  /A SER 2002 O      -0.353    2.773
    /A PRO 2083 O     /A THR 2043 N      -0.353    2.998
    /A LEU 2022 HB3   /A PRO 2058 HB2    -0.354    2.354
    /A PRO 2058 CD    /A LEU 2022 HD21   -0.357    3.057
    /A LEU 2022 O     /A ARG 2056 CA     -0.358    3.478
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.361    3.061
    /A ARG 2059 C     /A ASN 2080 H      -0.361    2.971
    /A ARG 2026 N     /A VAL 2000 O      -0.361    3.006
    /A ILE 2060 CG2   /A PHE 2077 CE2    -0.363    3.763
    /A LEU 2041 CG    /A ASP 2038 HB3    -0.363    3.063
    /A ARG 2059 CB    /A ASN 2080 HB3    -0.365    3.065
    /A ILE 2079 HG13  /A ILE 2060 HG22   -0.365    2.365
    /A ILE 2025 CB    /A LEU 2022 HD22   -0.366    3.066
    /A GLY 2023 N     /A LEU 2022 HG     -0.366    2.991
    /A GLU 2021 CB    /A ARG 2056 HD3    -0.366    3.066
    /A THR 2085 C     /A ILE 2086 HG13   -0.367    2.977
    /A ASN 2080 ND2   /A GLU 2078 CG     -0.367    3.692
    /A VAL 2057 CB    /A PRO 2058 CG     -0.369    3.769
    /A VAL 2057 CG2   /A ASN 2024 CA     -0.369    3.769
    /A ASN 2080 OD1   /A GLU 2078 OE1    -0.371    3.211
    /A LEU 2041 C     /A THR 2085 H      -0.373    2.983
    /A GLU 2021 O     /A LEU 2005 N      -0.373    3.018
    /A GLU 2021 OE2   /A ARG 2056 NE     -0.374    3.019
    /A ILE 2025 CA    /A VAL 2000 O      -0.375    3.495
    /A ASN 2080 CB    /A ARG 2059 HB3    -0.377    3.077
    /A ILE 2025 CG1   /A LEU 2001 CD2    -0.385    3.785
    /A LEU 2022 CD2   /A LEU 2001 CD2    -0.386    3.786
    /A ILE 2060 O     /A LEU 2019 HD11   -0.388    2.808
    /A ILE 2079 HD12  /A ILE 2181 CD1    -0.389    3.089
    /A ILE 2025 HD12  /A LEU 2040 HD21   -0.390    2.390
    /A ILE 2084 H     /A ILE 2084 HG12   -0.390    2.390
    /A ILE 2079 O     /A ILE 2181 CG2    -0.390    3.510
    /A PRO 2058 CD    /A LEU 2022 CB     -0.391    3.791
    /A ILE 2084 CG1   /A ILE 2086 HG13   -0.391    3.091
    /A THR 2085 OG1   /A ARG 2187 HD2    -0.392    2.892
    /A ILE 2025 HD13  /A LEU 2040 CD2    -0.392    3.092
    /A LEU 2041 HB2   /A THR 2085 HB     -0.392    2.392
    /A ILE 2025 HD12  /A LEU 2040 CD2    -0.392    3.092
    /A VAL 2057 O     /A PRO 2058 HG2    -0.393    2.813
    /A LEU 2020 O     /A GLU 2021 CG     -0.393    3.513
    /A ARG 2026 C     /A VAL 2000 H      -0.393    3.003
    /A ILE 2025 HG12  /A LEU 1999 HD13   -0.394    2.394
    /A ASN 2080 OD1   /A PRO 2182 CD     -0.395    3.515
    /A ILE 2079 N     /A LYS 2180 O      -0.399    3.044
    /A THR 2085 N     /A THR 2043 OG1    -0.399    3.124
    /A PRO 2058 CG    /A LEU 2022 HB3    -0.400    3.100
    

  
323 contacts  

> ui tool show Contacts

> close #1.1

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel intraRes true ignoreHiddenModels true color #ffffff dashes 4
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    323 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 CB    /A PRO 2058 HD2    1.082    1.618
    /A VAL 2057 CG1   /A PRO 2058 HD2    0.984    1.716
    /A GLU 2021 CD    /A ARG 2056 NH1    0.716    2.789
    /A PRO 2083 HB3   /A ILE 2045 HD12   0.629    1.371
    /A PRO 2058 CD    /A VAL 2057 HB     0.618    2.082
    /A PRO 2058 CD    /A VAL 2057 CG1    0.603    2.797
    /A THR 2085 HG1   /A THR 2043 OG1    0.505    1.595
    /A GLU 2021 CD    /A ARG 2056 CZ     0.496    2.994
    /A PRO 2058 HD2   /A VAL 2057 HB     0.482    1.518
    /A GLU 2021 OE2   /A ARG 2056 CZ     0.469    2.561
    /A ALA 2082 O     /A ILE 2084 HG22   0.435    1.985
    /A GLU 2021 OE1   /A ARG 2056 NH1    0.430    2.215
    /A ASN 2080 OD1   /A PRO 2182 HG2    0.403    2.017
    /A PRO 2083 HB3   /A ILE 2045 CD1    0.352    2.348
    /A VAL 2057 HG23  /A ASN 2024 HA     0.336    1.664
    /A VAL 2057 HG12  /A ILE 2025 HG21   0.327    1.673
    /A ASN 2024 HB3   /A SER 2002 OG     0.311    2.189
    /A PRO 2083 CB    /A ILE 2045 HD12   0.299    2.401
    /A LEU 2041 CD2   /A ARG 2026 HG3    0.297    2.403
    /A THR 2085 HG1   /A THR 2043 CB     0.286    2.414
    /A ASN 2080 HD22  /A GLU 2078 CD     0.273    2.607
    /A ASN 2080 H     /A ARG 2059 O      0.258    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.249    2.871
    /A THR 2085 H     /A LEU 2041 O      0.230    1.790
    /A ARG 2026 O     /A VAL 2000 H      0.204    1.816
    /A VAL 2057 HG13  /A PRO 2058 HD2    0.201    1.799
    /A ILE 2060 H     /A LEU 2020 O      0.195    1.825
    /A VAL 2057 HG12  /A PRO 2058 HD2    0.194    1.806
    /A ILE 2025 CG2   /A VAL 2057 HG12   0.191    2.509
    /A ARG 2026 HA    /A LEU 2040 O      0.189    2.231
    /A GLU 2021 H     /A LEU 2005 O      0.173    1.847
    /A ILE 2060 O     /A LEU 2020 H      0.170    1.850
    /A ALA 2082 H     /A VAL 2057 O      0.168    1.852
    /A VAL 2057 O     /A VAL 2057 HG13   0.156    2.264
    /A ILE 2084 HG21  /A ILE 2084 HD11   0.156    1.844
    /A ASN 2080 O     /A ARG 2059 H      0.148    1.872
    /A ASN 2024 CB    /A SER 2002 OG     0.136    3.064
    /A LEU 2020 O     /A ARG 2059 HA     0.122    2.298
    /A ARG 2059 HE    /A LEU 2019 HD13   0.121    1.879
    /A ILE 2079 O     /A PRO 2182 HD3    0.120    2.300
    /A ARG 2026 NH2   /A GLU 2028 OE1    0.119    2.526
    /A ALA 2082 O     /A VAL 2081 HG11   0.113    2.307
    /A PRO 2083 HB2   /A THR 2043 O      0.108    2.312
    /A LEU 2020 C     /A LEU 2020 HD21   0.098    2.512
    /A ASN 2080 OD1   /A PRO 2182 CG     0.098    3.022
    /A LEU 2041 HD13  /A ASP 2038 CG     0.096    2.784
    /A ILE 2079 HD11  /A PHE 2077 CE1    0.091    2.609
    /A ILE 2084 O     /A ILE 2084 HG13   0.085    2.335
    /A PRO 2083 CB    /A ILE 2045 CD1    0.084    3.316
    /A GLU 2021 OE1   /A ARG 2056 CZ     0.084    2.946
    /A THR 2085 H     /A THR 2043 HG1    0.084    1.916
    /A VAL 2057 CG1   /A ILE 2025 HG21   0.083    2.617
    /A PRO 2083 HA    /A PRO 2185 O      0.076    2.344
    /A ALA 2082 O     /A ILE 2084 CG2    0.072    3.048
    /A ARG 2026 CG    /A LEU 2041 CD2    0.064    3.336
    /A THR 2085 OG1   /A THR 2043 OG1    0.058    2.542
    /A ILE 2060 HA    /A GLU 2078 O      0.053    2.367
    /A PRO 2058 HG3   /A LEU 2022 HD21   0.053    1.947
    /A GLU 2021 CD    /A ARG 2056 NE     0.052    3.453
    /A THR 2085 HA    /A ARG 2187 O      0.051    2.369
    /A ARG 2059 HD2   /A ARG 2059 HH11   0.047    1.953
    /A ILE 2084 O     /A ARG 2187 H      0.043    1.977
    /A THR 2085 HG1   /A THR 2043 CG2    0.042    2.658
    /A THR 2085 CB    /A THR 2043 OG1    0.038    3.162
    /A ILE 2084 HD12  /A ILE 2086 CG1    0.027    2.673
    /A THR 2085 O     /A LEU 2040 HA     0.026    2.394
    /A PRO 2058 HD3   /A LEU 2022 HB3    0.025    1.975
    /A PRO 2083 O     /A THR 2043 H      0.023    1.997
    /A ARG 2026 CZ    /A GLU 2028 OE1    0.021    3.009
    /A PRO 2058 O     /A LEU 2022 H      0.018    2.002
    /A ILE 2084 CD1   /A ILE 2086 CD1    0.015    3.385
    /A PRO 2058 HD3   /A VAL 2057 HB     0.015    1.985
    /A LEU 2041 HD23  /A ARG 2026 HG3    0.013    1.987
    /A ILE 2079 HD11  /A PHE 2077 HE1    0.013    1.987
    /A LEU 2041 HD22  /A ARG 2026 HG3    0.013    1.987
    /A ASN 2080 ND2   /A GLU 2078 CD     0.011    3.494
    /A THR 2085 N     /A THR 2043 HG1    0.011    2.614
    /A GLU 2021 CD    /A ARG 2056 NH2    0.010    3.495
    /A ARG 2059 HE    /A LEU 2019 CD1    0.010    2.690
    /A ILE 2084 HD12  /A LEU 2040 CD1    0.009    2.691
    /A GLU 2021 O     /A LEU 2005 H      0.008    2.012
    /A LEU 2041 CD1   /A ASP 2038 HB3    0.006    2.694
    /A LEU 2041 HD13  /A ASP 2038 CB     -0.001    2.701
    /A ASN 2080 HD22  /A GLU 2078 OE1    -0.004    2.024
    /A ASN 2080 HB3   /A ARG 2059 HB3    -0.009    2.009
    /A PRO 2058 CD    /A VAL 2057 HG13   -0.013    2.713
    /A PRO 2058 CD    /A VAL 2057 HG12   -0.013    2.713
    /A VAL 2057 CG2   /A ASN 2024 HA     -0.023    2.723
    /A ARG 2026 H     /A VAL 2000 O      -0.023    2.043
    /A LEU 2022 CD2   /A ILE 2025 HB     -0.023    2.723
    /A THR 2085 OG1   /A ARG 2187 HB3    -0.027    2.527
    /A ILE 2084 CD1   /A ILE 2086 CG1    -0.028    3.428
    /A ILE 2079 HG21  /A ILE 2079 HD13   -0.029    2.029
    /A ILE 2084 HD12  /A LEU 2040 HD12   -0.031    2.031
    /A ILE 2025 HG23  /A ILE 2025 HD13   -0.032    2.032
    /A VAL 2057 HG23  /A ASN 2024 CA     -0.037    2.737
    /A LEU 2022 O     /A VAL 2057 H      -0.039    2.059
    /A ILE 2079 O     /A PRO 2182 CD     -0.040    3.160
    /A GLY 2023 O     /A VAL 2057 HG23   -0.045    2.465
    /A GLY 2023 O     /A VAL 2057 HG22   -0.046    2.466
    /A ILE 2025 HB    /A LEU 2022 HD22   -0.047    2.047
    /A ILE 2084 O     /A VAL 2186 HA     -0.047    2.467
    /A ARG 2026 O     /A LEU 1999 HD11   -0.059    2.479
    /A GLY 2023 HA3   /A ALA 2003 HB2    -0.061    2.061
    /A GLU 2021 OE2   /A ARG 2056 NH2    -0.061    2.706
    /A LEU 2022 HD13  /A LEU 2001 HB3    -0.066    2.066
    /A LEU 2041 HD13  /A ASP 2038 HB3    -0.066    2.066
    /A ILE 2079 H     /A LYS 2180 O      -0.068    2.088
    /A ILE 2025 CD1   /A LEU 2040 CD2    -0.069    3.469
    /A ILE 2060 HG21  /A ILE 2060 HD13   -0.076    2.076
    /A GLU 2021 CD    /A ARG 2056 HH11   -0.077    2.957
    /A ARG 2026 HH21  /A GLU 2028 OE1    -0.078    2.098
    /A THR 2085 O     /A LEU 2041 H      -0.080    2.100
    /A ARG 2026 O     /A LEU 1999 HA     -0.082    2.502
    /A ILE 2025 CD1   /A LEU 2040 HD21   -0.085    2.785
    /A ILE 2084 CD1   /A LEU 2040 HD12   -0.085    2.785
    /A ILE 2060 O     /A LEU 2019 HA     -0.089    2.509
    /A ALA 2082 CB    /A VAL 2057 HA     -0.091    2.791
    /A PRO 2058 O     /A GLU 2021 HA     -0.095    2.515
    /A ILE 2025 HA    /A VAL 2000 O      -0.096    2.516
    /A PRO 2058 CD    /A LEU 2022 HB3    -0.097    2.797
    /A LEU 2020 HD21  /A GLU 2021 N      -0.097    2.722
    /A LEU 2020 HB3   /A ILE 2060 HB     -0.100    2.100
    /A ARG 2026 CA    /A LEU 2040 O      -0.102    3.222
    /A ILE 2079 O     /A ILE 2181 HG22   -0.102    2.522
    /A VAL 2081 HB    /A VAL 2184 HG22   -0.103    2.103
    /A LEU 2041 O     /A THR 2085 N      -0.104    2.749
    /A VAL 2057 O     /A VAL 2081 HA     -0.105    2.525
    /A ILE 2079 CD1   /A PHE 2077 CE1    -0.105    3.505
    /A ASN 2080 O     /A PRO 2058 HA     -0.106    2.526
    /A LEU 2041 O     /A ILE 2084 HA     -0.106    2.526
    /A ARG 2059 O     /A ASN 2080 N      -0.107    2.752
    /A ALA 2042 C     /A THR 2043 HG1    -0.108    2.718
    /A VAL 2057 CG1   /A PRO 2058 CG     -0.112    3.512
    /A LEU 2041 CD1   /A ASP 2038 CB     -0.113    3.513
    /A PRO 2058 HD3   /A VAL 2057 CB     -0.115    2.815
    /A ILE 2025 O     /A ILE 2025 HG22   -0.117    2.537
    /A ILE 2025 CG2   /A VAL 2057 CG1    -0.121    3.521
    /A PRO 2083 CD    /A ALA 2082 HB1    -0.122    2.822
    /A THR 2085 OG1   /A THR 2043 CB     -0.122    3.322
    /A THR 2085 OG1   /A THR 2043 HG21   -0.134    2.634
    /A PRO 2058 CG    /A LEU 2022 HD21   -0.135    2.835
    /A LEU 2022 CD2   /A LEU 2001 HD23   -0.135    2.835
    /A ARG 2026 CG    /A LEU 2041 HD22   -0.139    2.839
    /A GLU 2021 O     /A PHE 2004 HA     -0.139    2.559
    /A GLU 2021 CD    /A ARG 2056 CD     -0.141    3.721
    /A LEU 2041 HG    /A LEU 2040 C      -0.142    2.752
    /A ALA 2082 HA    /A PRO 2083 HD2    -0.144    2.144
    /A PRO 2058 HD3   /A LEU 2022 CB     -0.144    2.844
    /A LEU 2020 O     /A ARG 2059 CA     -0.146    3.266
    /A LEU 2022 HD22  /A LEU 2001 HD23   -0.148    2.148
    /A THR 2085 HG1   /A THR 2043 HG1    -0.151    2.151
    /A THR 2085 OG1   /A THR 2043 CG2    -0.155    3.355
    /A VAL 2057 HA    /A ALA 2082 HB2    -0.156    2.156
    /A VAL 2081 HG21  /A ILE 2079 HG23   -0.159    2.159
    /A ILE 2079 HB    /A ILE 2181 HG13   -0.159    2.159
    /A GLU 2021 CD    /A ARG 2056 HH12   -0.159    3.039
    /A PRO 2083 HB3   /A ILE 2045 CG1    -0.161    2.861
    /A ALA 2082 N     /A VAL 2081 HG11   -0.163    2.788
    /A GLY 2023 H     /A SER 2002 O      -0.163    2.183
    /A LEU 2041 O     /A ILE 2084 CA     -0.164    3.284
    /A ARG 2026 O     /A VAL 2000 N      -0.169    2.814
    /A ARG 2026 CG    /A LEU 2041 HD23   -0.169    2.869
    /A LEU 2022 O     /A VAL 2057 N      -0.170    2.815
    /A LEU 2020 O     /A ILE 2060 N      -0.172    2.817
    /A LEU 2020 HA    /A LEU 2005 O      -0.173    2.593
    /A THR 2085 CA    /A ARG 2187 O      -0.173    3.293
    /A LEU 2022 HA    /A LEU 2022 HD11   -0.175    2.175
    /A ILE 2084 HG22  /A PRO 2083 C      -0.176    2.786
    /A GLU 2021 CD    /A ARG 2056 HD3    -0.176    3.056
    /A ILE 2025 H     /A ASN 2024 OD1    -0.178    2.198
    /A ASN 2024 HB3   /A SER 2002 HG     -0.178    2.178
    /A VAL 2081 CG2   /A ILE 2079 HG23   -0.180    2.880
    /A GLU 2021 HB3   /A ARG 2056 HD3    -0.183    2.183
    /A ASN 2024 O     /A SER 2002 H      -0.184    2.204
    /A PRO 2083 CA    /A PRO 2185 O      -0.184    3.304
    /A GLU 2021 N     /A LEU 2005 O      -0.185    2.830
    /A ILE 2060 HG12  /A ILE 2079 HG22   -0.190    2.190
    /A LEU 2020 HD12  /A PHE 2004 HE2    -0.192    2.192
    /A THR 2085 HG1   /A THR 2043 HG21   -0.194    2.194
    /A ILE 2084 HD12  /A ILE 2086 HG12   -0.197    2.197
    /A GLU 2021 OE1   /A ARG 2056 HH12   -0.197    2.217
    /A ILE 2079 CD1   /A PHE 2077 HE1    -0.200    2.900
    /A LEU 2022 CD1   /A LEU 2001 HB3    -0.200    2.900
    /A ILE 2060 CA    /A GLU 2078 O      -0.201    3.321
    /A ILE 2084 CG1   /A VAL 2186 HG11   -0.202    2.902
    /A LEU 2041 HD22  /A LEU 2041 HA     -0.205    2.205
    /A ILE 2025 HG13  /A LEU 2040 HD21   -0.206    2.206
    /A ASN 2024 O     /A LEU 2001 HA     -0.208    2.628
    /A LEU 2020 N     /A ILE 2060 O      -0.212    2.857
    /A VAL 2057 O     /A ALA 2082 N      -0.214    2.859
    /A VAL 2081 HB    /A VAL 2184 CG2    -0.222    2.922
    /A ARG 2026 NH2   /A GLU 2028 CD     -0.223    3.728
    /A ILE 2025 HG12  /A LEU 2001 CD2    -0.223    2.923
    /A GLU 2021 OE2   /A ARG 2056 NH1    -0.226    2.871
    /A ASN 2080 O     /A ARG 2059 N      -0.227    2.872
    /A ILE 2025 CG1   /A LEU 2040 HD21   -0.229    2.929
    /A LEU 2022 HD22  /A LEU 2001 CD2    -0.231    2.931
    /A LEU 2020 HB2   /A TYR 2006 HD2    -0.232    2.232
    /A ILE 2084 CD1   /A LEU 2040 CD1    -0.232    3.632
    /A ASN 2024 OD1   /A ILE 2025 N      -0.233    2.878
    /A GLU 2021 OE1   /A LEU 2019 HD23   -0.237    2.657
    /A ILE 2079 HD11  /A PHE 2077 CZ     -0.239    2.939
    /A ILE 2079 O     /A ILE 2181 HA     -0.241    2.661
    /A ILE 2025 HG12  /A LEU 2001 HD21   -0.241    2.241
    /A ARG 2059 NE    /A LEU 2019 HD13   -0.243    2.868
    /A GLU 2021 HG3   /A LEU 2019 HG     -0.243    2.243
    /A ILE 2084 O     /A VAL 2186 CA     -0.246    3.366
    /A LEU 2041 HG    /A LEU 2040 O      -0.249    2.669
    /A ILE 2084 HD13  /A ILE 2086 CD1    -0.250    2.950
    /A ALA 2082 HB1   /A PRO 2083 HD3    -0.251    2.251
    /A ILE 2084 HD12  /A ILE 2086 CD1    -0.251    2.951
    /A ARG 2059 O     /A ILE 2079 HA     -0.253    2.673
    /A LEU 2020 CD2   /A GLU 2021 N      -0.254    3.579
    /A LEU 2041 CD2   /A ARG 2026 CD     -0.255    3.655
    /A ARG 2026 HH21  /A GLU 2028 CD     -0.261    3.141
    /A ILE 2084 HG13  /A ILE 2086 HG13   -0.261    2.261
    /A LEU 2041 CD1   /A ASP 2038 CG     -0.261    3.841
    /A LEU 2041 CG    /A LEU 2040 O      -0.262    3.382
    /A THR 2085 O     /A LEU 2040 CA     -0.262    3.382
    /A GLU 2021 HG2   /A ARG 2059 HG3    -0.264    2.264
    /A PRO 2083 CB    /A THR 2043 O      -0.268    3.388
    /A PRO 2058 O     /A LEU 2022 N      -0.268    2.913
    /A ILE 2025 CG1   /A LEU 1999 HD13   -0.269    2.969
    /A ASN 2024 CG    /A ILE 2025 H      -0.272    2.882
    /A GLU 2021 CD    /A LEU 2019 HD23   -0.273    3.153
    /A GLY 2023 CA    /A SER 2002 O      -0.273    3.393
    /A LEU 2022 HD13  /A LEU 2001 CB     -0.274    2.974
    /A VAL 2081 CG1   /A ALA 2082 O      -0.274    3.394
    /A LEU 2022 O     /A PRO 2058 HD3    -0.277    2.697
    /A ARG 2026 HD3   /A ARG 2026 HH11   -0.280    2.280
    /A PRO 2083 CB    /A ILE 2045 CG1    -0.282    3.682
    /A LEU 2022 O     /A PRO 2058 CD     -0.283    3.403
    /A GLU 2021 OE1   /A ARG 2056 HH11   -0.284    2.304
    /A VAL 2081 O     /A VAL 2184 HG23   -0.284    2.704
    /A LEU 2022 O     /A PRO 2058 N      -0.286    3.346
    /A LEU 2022 HD12  /A PHE 2004 HD2    -0.289    2.289
    /A PRO 2083 CG    /A ILE 2045 HD12   -0.289    2.989
    /A ARG 2026 HB3   /A VAL 2000 HB     -0.290    2.290
    /A THR 2085 HG23  /A ILE 2086 N      -0.291    2.916
    /A LEU 2020 C     /A GLU 2021 HG3    -0.291    2.901
    /A ASN 2080 ND2   /A GLU 2078 HG3    -0.292    2.917
    /A ILE 2084 HG12  /A VAL 2186 HG11   -0.292    2.292
    /A LEU 2022 CD2   /A PRO 2058 HG3    -0.297    2.997
    /A ILE 2079 N     /A GLU 2078 HG3    -0.298    2.923
    /A THR 2085 HA    /A ARG 2187 HB3    -0.302    2.302
    /A VAL 2057 C     /A ALA 2082 H      -0.307    2.917
    /A ASN 2024 CB    /A SER 2002 HG     -0.308    3.008
    /A LEU 2020 HD21  /A LEU 2020 O      -0.308    2.728
    /A ARG 2026 O     /A LEU 1999 CA     -0.309    3.429
    /A LEU 2041 O     /A THR 2043 HG1    -0.310    2.330
    /A ILE 2025 CD1   /A LEU 1999 HD13   -0.311    3.011
    /A ILE 2084 O     /A ARG 2187 N      -0.312    2.957
    /A ASN 2080 ND2   /A GLU 2078 OE1    -0.313    2.958
    /A GLY 2023 N     /A SER 2002 O      -0.315    2.960
    /A LEU 2041 HD23  /A ARG 2026 CD     -0.316    3.016
    /A LEU 2020 CD1   /A PHE 2004 HE2    -0.318    3.018
    /A ILE 2060 HG23  /A PHE 2061 N      -0.321    2.946
    /A VAL 2081 O     /A VAL 2184 HG13   -0.322    2.742
    /A ARG 2026 HG2   /A MET 2027 N      -0.325    2.950
    /A ILE 2060 O     /A LEU 2019 CA     -0.325    3.445
    /A GLY 2023 CA    /A ALA 2003 HB2    -0.326    3.026
    /A PRO 2083 CB    /A ILE 2045 HG13   -0.326    3.026
    /A THR 2085 OG1   /A ARG 2187 CB     -0.327    3.527
    /A ASN 2080 C     /A VAL 2081 HG21   -0.327    2.937
    /A PRO 2083 CG    /A ILE 2045 CD1    -0.330    3.730
    /A ASN 2024 H     /A SER 2002 O      -0.334    2.354
    /A VAL 2057 O     /A VAL 2081 CA     -0.336    3.456
    /A ILE 2084 CG2   /A PRO 2083 O      -0.337    3.457
    /A ILE 2079 CG1   /A PHE 2077 CE1    -0.339    3.739
    /A GLU 2021 CA    /A PRO 2058 O      -0.342    3.462
    /A ARG 2059 NE    /A LEU 2019 CD1    -0.342    3.667
    /A LEU 2041 HD23  /A ARG 2026 NE     -0.343    2.968
    /A PRO 2058 CA    /A ASN 2080 O      -0.344    3.464
    /A LEU 2020 C     /A ILE 2060 H      -0.344    2.954
    /A ARG 2026 N     /A ILE 2025 HG13   -0.346    2.971
    /A ALA 2042 CB    /A VAL 2057 HG21   -0.353    3.053
    /A LEU 2022 HD11  /A SER 2002 O      -0.353    2.773
    /A PRO 2083 O     /A THR 2043 N      -0.353    2.998
    /A LEU 2022 HB3   /A PRO 2058 HB2    -0.354    2.354
    /A PRO 2058 CD    /A LEU 2022 HD21   -0.357    3.057
    /A LEU 2022 O     /A ARG 2056 CA     -0.358    3.478
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.361    3.061
    /A ARG 2059 C     /A ASN 2080 H      -0.361    2.971
    /A ARG 2026 N     /A VAL 2000 O      -0.361    3.006
    /A ILE 2060 CG2   /A PHE 2077 CE2    -0.363    3.763
    /A LEU 2041 CG    /A ASP 2038 HB3    -0.363    3.063
    /A ARG 2059 CB    /A ASN 2080 HB3    -0.365    3.065
    /A ILE 2079 HG13  /A ILE 2060 HG22   -0.365    2.365
    /A ILE 2025 CB    /A LEU 2022 HD22   -0.366    3.066
    /A GLY 2023 N     /A LEU 2022 HG     -0.366    2.991
    /A GLU 2021 CB    /A ARG 2056 HD3    -0.366    3.066
    /A THR 2085 C     /A ILE 2086 HG13   -0.367    2.977
    /A ASN 2080 ND2   /A GLU 2078 CG     -0.367    3.692
    /A VAL 2057 CB    /A PRO 2058 CG     -0.369    3.769
    /A VAL 2057 CG2   /A ASN 2024 CA     -0.369    3.769
    /A ASN 2080 OD1   /A GLU 2078 OE1    -0.371    3.211
    /A LEU 2041 C     /A THR 2085 H      -0.373    2.983
    /A GLU 2021 O     /A LEU 2005 N      -0.373    3.018
    /A GLU 2021 OE2   /A ARG 2056 NE     -0.374    3.019
    /A ILE 2025 CA    /A VAL 2000 O      -0.375    3.495
    /A ASN 2080 CB    /A ARG 2059 HB3    -0.377    3.077
    /A ILE 2025 CG1   /A LEU 2001 CD2    -0.385    3.785
    /A LEU 2022 CD2   /A LEU 2001 CD2    -0.386    3.786
    /A ILE 2060 O     /A LEU 2019 HD11   -0.388    2.808
    /A ILE 2079 HD12  /A ILE 2181 CD1    -0.389    3.089
    /A ILE 2025 HD12  /A LEU 2040 HD21   -0.390    2.390
    /A ILE 2084 H     /A ILE 2084 HG12   -0.390    2.390
    /A ILE 2079 O     /A ILE 2181 CG2    -0.390    3.510
    /A PRO 2058 CD    /A LEU 2022 CB     -0.391    3.791
    /A ILE 2084 CG1   /A ILE 2086 HG13   -0.391    3.091
    /A THR 2085 OG1   /A ARG 2187 HD2    -0.392    2.892
    /A ILE 2025 HD13  /A LEU 2040 CD2    -0.392    3.092
    /A LEU 2041 HB2   /A THR 2085 HB     -0.392    2.392
    /A ILE 2025 HD12  /A LEU 2040 CD2    -0.392    3.092
    /A VAL 2057 O     /A PRO 2058 HG2    -0.393    2.813
    /A LEU 2020 O     /A GLU 2021 CG     -0.393    3.513
    /A ARG 2026 C     /A VAL 2000 H      -0.393    3.003
    /A ILE 2025 HG12  /A LEU 1999 HD13   -0.394    2.394
    /A ASN 2080 OD1   /A PRO 2182 CD     -0.395    3.515
    /A ILE 2079 N     /A LYS 2180 O      -0.399    3.044
    /A THR 2085 N     /A THR 2043 OG1    -0.399    3.124
    /A PRO 2058 CG    /A LEU 2022 HB3    -0.400    3.100
    

  
323 contacts  

> close #1.1

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> select clear

> select /A:2020-2027

134 atoms, 133 bonds, 8 residues, 1 model selected  

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 20 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 4 pseudobonds, 20 residues, 2 models selected  

> close #1.1

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    130 contacts
         atom1             atom2        overlap  distance
    /A PRO 2058 HD2   /A VAL 2057 CB     1.082    1.618
    /A PRO 2058 HD2   /A VAL 2057 CG1    0.984    1.716
    /A VAL 2057 HB    /A PRO 2058 CD     0.618    2.082
    /A VAL 2057 CG1   /A PRO 2058 CD     0.603    2.797
    /A VAL 2057 HB    /A PRO 2058 HD2    0.482    1.518
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A PRO 2058 HD2   /A VAL 2057 HG13   0.201    1.799
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A PRO 2058 HD2   /A VAL 2057 HG12   0.194    1.806
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2022 HD21  /A PRO 2058 HG3    0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HB3   /A PRO 2058 HD3    0.025    1.975
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A VAL 2057 HB    /A PRO 2058 HD3    0.015    1.985
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A VAL 2057 HG13  /A PRO 2058 CD     -0.013    2.713
    /A VAL 2057 HG12  /A PRO 2058 CD     -0.013    2.713
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A LEU 2022 HB3   /A PRO 2058 CD     -0.097    2.797
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A PRO 2058 CG    /A VAL 2057 CG1    -0.112    3.512
    /A VAL 2057 CB    /A PRO 2058 HD3    -0.115    2.815
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2022 HD21  /A PRO 2058 CG     -0.135    2.835
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A LEU 2022 CB    /A PRO 2058 HD3    -0.144    2.844
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A PRO 2058 HD3   /A LEU 2022 O      -0.277    2.697
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A PRO 2058 CD    /A LEU 2022 O      -0.283    3.403
    /A PRO 2058 N     /A LEU 2022 O      -0.286    3.346
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 HG3   /A LEU 2022 CD2    -0.297    2.997
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A PRO 2058 HB2   /A LEU 2022 HB3    -0.354    2.354
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.357    3.057
    /A LEU 2022 HB3   /A PRO 2058 CB     -0.361    3.061
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A PRO 2058 CG    /A VAL 2057 CB     -0.369    3.769
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A LEU 2022 CB    /A PRO 2058 CD     -0.391    3.791
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A PRO 2058 HG2   /A VAL 2057 O      -0.393    2.813
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.400    3.100
    

  
130 contacts  

> name frozen Contacts sel

> select clear

> select Contacts

146 atoms, 74 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> select clear

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2022-2023

26 atoms, 25 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> select /A:2022-2023

26 atoms, 25 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2022-2023

26 atoms, 25 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> select clear

> select /A:2025

19 atoms, 18 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2025

19 atoms, 18 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> close #1.1

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    130 contacts
         atom1             atom2        overlap  distance
    /A PRO 2058 HD2   /A VAL 2057 CB     1.082    1.618
    /A PRO 2058 HD2   /A VAL 2057 CG1    0.984    1.716
    /A VAL 2057 HB    /A PRO 2058 CD     0.618    2.082
    /A VAL 2057 CG1   /A PRO 2058 CD     0.603    2.797
    /A VAL 2057 HB    /A PRO 2058 HD2    0.482    1.518
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A PRO 2058 HD2   /A VAL 2057 HG13   0.201    1.799
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A PRO 2058 HD2   /A VAL 2057 HG12   0.194    1.806
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2022 HD21  /A PRO 2058 HG3    0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HB3   /A PRO 2058 HD3    0.025    1.975
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A VAL 2057 HB    /A PRO 2058 HD3    0.015    1.985
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A VAL 2057 HG13  /A PRO 2058 CD     -0.013    2.713
    /A VAL 2057 HG12  /A PRO 2058 CD     -0.013    2.713
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A LEU 2022 HB3   /A PRO 2058 CD     -0.097    2.797
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A PRO 2058 CG    /A VAL 2057 CG1    -0.112    3.512
    /A VAL 2057 CB    /A PRO 2058 HD3    -0.115    2.815
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2022 HD21  /A PRO 2058 CG     -0.135    2.835
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A LEU 2022 CB    /A PRO 2058 HD3    -0.144    2.844
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A PRO 2058 HD3   /A LEU 2022 O      -0.277    2.697
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A PRO 2058 CD    /A LEU 2022 O      -0.283    3.403
    /A PRO 2058 N     /A LEU 2022 O      -0.286    3.346
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 HG3   /A LEU 2022 CD2    -0.297    2.997
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A PRO 2058 HB2   /A LEU 2022 HB3    -0.354    2.354
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.357    3.057
    /A LEU 2022 HB3   /A PRO 2058 CB     -0.361    3.061
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A PRO 2058 CG    /A VAL 2057 CB     -0.369    3.769
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A LEU 2022 CB    /A PRO 2058 CD     -0.391    3.791
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A PRO 2058 HG2   /A VAL 2057 O      -0.393    2.813
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.400    3.100
    

  
130 contacts  

> name frozen Contacts sel

> select clear

> select Contacts

146 atoms, 74 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> swapaa /A: 2058 leu

Using Dunbrack library  
/A PRO 2058: phi -137.9, psi 132.6 trans  
Applying LEU rotamer (chi angles: 177.6 65.4) to /A LEU 2058  

> close #1.1-2

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

320 atoms, 317 bonds, 20 residues, 1 model selected  

> select /A:2120-2121

25 atoms, 24 bonds, 2 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

320 atoms, 317 bonds, 20 residues, 1 model selected  

> select /A:2120-2121

25 atoms, 24 bonds, 2 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

320 atoms, 317 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    112 contacts
         atom1             atom2        overlap  distance
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A VAL 2081 HG22  /A LEU 2058 CD1    0.269    2.611
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 H     /A LEU 2058 O      0.018    2.002
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A LEU 2058 CD1   /A ARG 2059 N      0.002    3.503
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2081 CG2   /A LEU 2058 CD1    -0.086    3.666
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A LEU 2058 CD1   /A ASN 2080 O      -0.095    3.395
    /A GLU 2021 HA    /A LEU 2058 O      -0.095    2.515
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A LEU 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A LEU 2058 CB    /A LEU 2022 HB3    -0.170    3.050
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A ARG 2059 H     /A LEU 2058 CD1    -0.240    3.120
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A LEU 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A ILE 2079 CG2   /A LEU 2058 CD1    -0.330    3.910
    /A LEU 2058 CG    /A ILE 2060 HG13   -0.330    3.210
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A LEU 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A LEU 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A ILE 2079 HG22  /A LEU 2058 CD1    -0.370    3.250
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A LEU 2058 CD2   /A ILE 2060 HD11   -0.375    3.255
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    

  
112 contacts  

> name frozen Contacts_leu sel

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> help help:user

> close #1.1-2

> swapaa /A: 2058 pro

Using Dunbrack library  
/A LEU 2058: phi -137.9, psi 132.6 trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /A PRO 2058  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    119 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 HB    /A PRO 2058 CD     0.804    2.076
    /A VAL 2057 CG1   /A PRO 2058 CD     0.792    2.788
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A VAL 2057 HG13  /A PRO 2058 CD     0.176    2.704
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 HG12  /A PRO 2058 CD     0.170    2.710
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A VAL 2057 CG1   /A PRO 2058 CG     0.082    3.498
    /A LEU 2022 HB3   /A PRO 2058 CD     0.073    2.807
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HD21  /A PRO 2058 CG     0.035    2.845
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A PRO 2058 CD    /A LEU 2022 O      -0.103    3.403
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A VAL 2057 CB    /A PRO 2058 CG     -0.176    3.756
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.185    3.065
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.189    3.069
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A LEU 2022 CB    /A PRO 2058 CD     -0.221    3.801
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.229    3.109
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A VAL 2057 HG13  /A PRO 2058 CG     -0.266    3.146
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A VAL 2057 HG12  /A PRO 2058 CG     -0.281    3.161
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 N     /A LEU 2022 O      -0.301    3.346
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A PRO 2058 CG    /A LEU 2022 CD2    -0.312    3.892
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    

  
119 contacts  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    2 clashes
        atom1            atom2       overlap  distance
    /A VAL 2057 HB  /A PRO 2058 CD    0.804    2.076
    /A PRO 2058 CD  /A VAL 2057 CG1   0.792    2.788
    

  
2 clashes  

> ui windowfill toggle

> select clear

> ui windowfill toggle

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> show sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> ui windowfill toggle

[Repeated 5 time(s)]

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> ui windowfill toggle

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    119 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 HB    /A PRO 2058 CD     0.804    2.076
    /A VAL 2057 CG1   /A PRO 2058 CD     0.792    2.788
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A VAL 2057 HG13  /A PRO 2058 CD     0.176    2.704
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 HG12  /A PRO 2058 CD     0.170    2.710
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A VAL 2057 CG1   /A PRO 2058 CG     0.082    3.498
    /A LEU 2022 HB3   /A PRO 2058 CD     0.073    2.807
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HD21  /A PRO 2058 CG     0.035    2.845
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A PRO 2058 CD    /A LEU 2022 O      -0.103    3.403
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A VAL 2057 CB    /A PRO 2058 CG     -0.176    3.756
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.185    3.065
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.189    3.069
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A LEU 2022 CB    /A PRO 2058 CD     -0.221    3.801
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.229    3.109
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A VAL 2057 HG13  /A PRO 2058 CG     -0.266    3.146
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A VAL 2057 HG12  /A PRO 2058 CG     -0.281    3.161
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 N     /A LEU 2022 O      -0.301    3.346
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A PRO 2058 CG    /A LEU 2022 CD2    -0.312    3.892
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    

  
119 contacts  

> ui windowfill toggle

[Repeated 3 time(s)]

> select clear

> ui windowfill toggle

> select /A:2078-2082

74 atoms, 73 bonds, 7 pseudobonds, 5 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> show sel cartoons

[Repeated 1 time(s)]

> hide sel cartoons

[Repeated 1 time(s)]

> show sel cartoons

> ui mousemode right select

Drag select of 272 atoms, 262 residues, 253 bonds, 33 pseudobonds  

> hide sel atoms

> show sel cartoons

[Repeated 1 time(s)]

> select clear

> close #1.1-2

> select /A:2058

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

> color sel orange

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 20 residues, 1 model selected  
Drag select of 2 residues  

> ui mousemode right translate

> swapaa /A: 2058 leu

Using Dunbrack library  
/A PRO 2058: phi -137.9, psi 132.6 trans  
Applying LEU rotamer (chi angles: 177.6 65.4) to /A LEU 2058  

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> save C:/Users/emirm/Desktop/contacts/Contacts.cxs

——— End of log from Tue Jul 29 15:17:34 2025 ———

> view name session-start

opened ChimeraX session  

> select /A:2058

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

> color sel red

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/ZoomedOut.tif width 1280 height 491
> supersample 3

> ui mousemode right select

Drag select of 262 residues  

> show sel surfaces

> transparency (#!1 & sel) 70

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOutSurface.tif width 1280 height
> 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
387556 of 3437070 triangles, 262 residues  

> hide sel surfaces

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to
fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
notes | Termini for fold_2025_02_26_14_57_hob_native_model_0.cif (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 2300  
Chain-final residues that are not actual C termini:  
1819 hydrogen bonds  
10 hydrogens added  
  

> ui windowfill toggle

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> select /A:2218

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:2218

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    134 contacts
         atom1             atom2        overlap  distance
    /A ILE 2084 HG22  /A ALA 2082 O      0.495    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2059 O     /A ASN 2080 H      0.318    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.309    2.871
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A LEU 2041 O     /A THR 2085 H      0.290    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.255    1.825
    /A LEU 2020 H     /A ILE 2060 O      0.230    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.228    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.216    2.264
    /A ARG 2059 H     /A ASN 2080 O      0.208    1.872
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 HD21  /A LEU 2020 C      0.188    2.512
    /A ARG 2059 HA    /A LEU 2020 O      0.182    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.173    2.307
    /A LEU 2058 HD12  /A ASN 2080 O      0.171    2.309
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ILE 2084 HG13  /A ILE 2084 O      0.145    2.335
    /A ILE 2084 CG2   /A ALA 2082 O      0.132    3.048
    /A VAL 2081 HG22  /A LEU 2058 CD1    0.096    2.604
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A LEU 2022 H     /A LEU 2058 O      0.078    2.002
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2058 HA    /A LEU 2058 HD12   0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A VAL 2057 H     /A LEU 2022 O      0.021    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      0.015    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      0.014    2.466
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A LEU 2022 HB3   /A LEU 2058 HB2    -0.002    2.002
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A LEU 2041 H     /A THR 2085 O      -0.020    2.100
    /A LEU 2058 HG    /A ARG 2059 N      -0.021    2.646
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A GLU 2021 HA    /A LEU 2058 O      -0.035    2.515
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A THR 2085 N     /A LEU 2041 O      -0.044    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.045    2.525
    /A LEU 2058 HA    /A ASN 2080 O      -0.046    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.046    2.526
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ASN 2080 N     /A ARG 2059 O      -0.047    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.057    2.537
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2058 HD13  /A VAL 2081 HG22   -0.081    2.081
    /A PRO 2083 C     /A ILE 2084 HG22   -0.086    2.786
    /A ARG 2059 CA    /A LEU 2020 O      -0.086    3.266
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A ILE 2084 CA    /A LEU 2041 O      -0.104    3.284
    /A VAL 2057 N     /A LEU 2022 O      -0.110    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.112    2.817
    /A ASN 2024 OD1   /A ILE 2025 H      -0.118    2.198
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ILE 2060 O     /A LEU 2020 N      -0.152    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.154    2.859
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ARG 2059 N     /A ASN 2080 O      -0.167    2.872
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A ILE 2025 N     /A ASN 2024 OD1    -0.173    2.878
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A LEU 2058 CD1   /A ARG 2059 N      -0.181    3.506
    /A ILE 2025 H     /A ASN 2024 CG     -0.182    2.882
    /A ILE 2060 HD11  /A LEU 2058 HD21   -0.184    2.184
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A ILE 2079 HA    /A ARG 2059 O      -0.193    2.673
    /A GLU 2021 HG3   /A LEU 2020 C      -0.201    2.901
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A LEU 2022 N     /A LEU 2058 O      -0.208    2.913
    /A LEU 2058 CD1   /A ASN 2080 O      -0.211    3.391
    /A ALA 2082 O     /A VAL 2081 CG1    -0.214    3.394
    /A LEU 2058 HD12  /A ARG 2059 N      -0.216    2.841
    /A ALA 2082 H     /A VAL 2057 C      -0.217    2.917
    /A ARG 2059 H     /A LEU 2058 HD12   -0.233    2.233
    /A VAL 2081 HG21  /A ASN 2080 C      -0.237    2.937
    /A LEU 2020 O     /A LEU 2020 HD21   -0.248    2.728
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2060 H     /A LEU 2020 C      -0.254    2.954
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A VAL 2081 CG2   /A LEU 2058 CD1    -0.259    3.659
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2058 H     /A LEU 2022 O      -0.267    2.347
    /A ASN 2080 H     /A ARG 2059 C      -0.271    2.971
    /A VAL 2081 CA    /A VAL 2057 O      -0.276    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.277    3.457
    /A LEU 2058 HD21  /A ILE 2060 CD1    -0.280    2.980
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A LEU 2058 O     /A GLU 2021 CA     -0.282    3.462
    /A THR 2085 H     /A LEU 2041 C      -0.283    2.983
    /A ASN 2080 O     /A LEU 2058 CA     -0.284    3.464
    /A ILE 2079 HG22  /A LEU 2058 HD11   -0.300    2.300
    /A LEU 2058 HB2   /A LEU 2022 CB     -0.304    3.004
    /A LEU 2020 H     /A ILE 2060 C      -0.314    3.014
    /A ILE 2084 C     /A LEU 2041 O      -0.315    3.495
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A ILE 2060 HG13  /A ARG 2059 C      -0.333    3.033
    /A GLU 2021 CG    /A LEU 2020 O      -0.333    3.513
    /A ARG 2059 H     /A ASN 2080 C      -0.333    3.033
    /A ARG 2059 C     /A LEU 2020 O      -0.340    3.520
    /A LEU 2020 CD2   /A LEU 2020 O      -0.340    3.520
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A ILE 2084 HG22  /A ALA 2082 C      -0.348    3.048
    /A LEU 2058 CB    /A LEU 2022 HB3    -0.353    3.053
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ILE 2084 CB    /A LEU 2041 O      -0.357    3.537
    /A THR 2085 O     /A LEU 2041 N      -0.358    3.063
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A VAL 2057 CB    /A GLY 2023 O      -0.369    3.549
    /A LEU 2022 HG    /A ASN 2024 O      -0.372    2.852
    /A VAL 2057 CG2   /A GLY 2023 C      -0.375    3.775
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A LEU 2058 HD11  /A ILE 2079 CG2    -0.378    3.078
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A ILE 2079 CA    /A ARG 2059 O      -0.394    3.574
    /A ASN 2024 O     /A LEU 2022 CG     -0.396    3.576
    

  
134 contacts  

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[Repeated 1 time(s)]

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 134 pseudobonds, 20 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    10 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N  /A ILE 2060 O  /A LEU 2020 H  2.857  1.850
    /A LEU 2022 N  /A LEU 2058 O  /A LEU 2022 H  2.913  2.002
    /A LEU 2041 N  /A THR 2085 O  /A LEU 2041 H  3.063  2.100
    /A VAL 2057 N  /A LEU 2022 O  /A VAL 2057 H  2.815  2.059
    /A LEU 2058 N  /A LEU 2022 O  /A LEU 2058 H  3.346  2.347
    /A ARG 2059 N  /A ASN 2080 O  /A ARG 2059 H  2.872  1.872
    /A ILE 2060 N  /A LEU 2020 O  /A ILE 2060 H  2.817  1.825
    /A ASN 2080 N  /A ARG 2059 O  /A ASN 2080 H  2.752  1.762
    /A ALA 2082 N  /A VAL 2057 O  /A ALA 2082 H  2.859  1.852
    /A THR 2085 N  /A LEU 2041 O  /A THR 2085 H  2.749  1.790
    

  
10 hydrogen bonds found  

> select clear

> hide #1.4 models

> hide #1.3 models

> select subtract #1.3

Nothing selected  

> hide #1.2 models

> show #1.2 models

> ui windowfill toggle

> ui mousemode right translate

> save C:/Users/emirm/Desktop/contacts/l2058_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.2 models

> show #1.3 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.3 models

> select subtract #1.3

Nothing selected  

> show #1.4 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_hb.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/session_L2058.cxs

——— End of log from Wed Jul 30 08:19:51 2025 ———

> view name session-start

opened ChimeraX session  

> close #1.2-4

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> ui tool show Contacts

> contacts sel saveFile C:/Users/emirm/Desktop/contacts/l2058_con_file
> restrict both intraRes true ignoreHiddenModels true select true color
> #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    134 contacts
         atom1             atom2        overlap  distance
    /A ILE 2084 HG22  /A ALA 2082 O      0.495    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2059 O     /A ASN 2080 H      0.318    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.309    2.871
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A LEU 2041 O     /A THR 2085 H      0.290    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.255    1.825
    /A LEU 2020 H     /A ILE 2060 O      0.230    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.228    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.216    2.264
    /A ARG 2059 H     /A ASN 2080 O      0.208    1.872
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 HD21  /A LEU 2020 C      0.188    2.512
    /A ARG 2059 HA    /A LEU 2020 O      0.182    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.173    2.307
    /A LEU 2058 HD12  /A ASN 2080 O      0.171    2.309
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ILE 2084 HG13  /A ILE 2084 O      0.145    2.335
    /A ILE 2084 CG2   /A ALA 2082 O      0.132    3.048
    /A VAL 2081 HG22  /A LEU 2058 CD1    0.096    2.604
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A LEU 2022 H     /A LEU 2058 O      0.078    2.002
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2058 HA    /A LEU 2058 HD12   0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A VAL 2057 H     /A LEU 2022 O      0.021    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      0.015    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      0.014    2.466
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A LEU 2022 HB3   /A LEU 2058 HB2    -0.002    2.002
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A LEU 2041 H     /A THR 2085 O      -0.020    2.100
    /A LEU 2058 HG    /A ARG 2059 N      -0.021    2.646
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A GLU 2021 HA    /A LEU 2058 O      -0.035    2.515
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A THR 2085 N     /A LEU 2041 O      -0.044    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.045    2.525
    /A LEU 2058 HA    /A ASN 2080 O      -0.046    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.046    2.526
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ASN 2080 N     /A ARG 2059 O      -0.047    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.057    2.537
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2058 HD13  /A VAL 2081 HG22   -0.081    2.081
    /A PRO 2083 C     /A ILE 2084 HG22   -0.086    2.786
    /A ARG 2059 CA    /A LEU 2020 O      -0.086    3.266
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A ILE 2084 CA    /A LEU 2041 O      -0.104    3.284
    /A VAL 2057 N     /A LEU 2022 O      -0.110    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.112    2.817
    /A ASN 2024 OD1   /A ILE 2025 H      -0.118    2.198
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ILE 2060 O     /A LEU 2020 N      -0.152    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.154    2.859
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ARG 2059 N     /A ASN 2080 O      -0.167    2.872
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A ILE 2025 N     /A ASN 2024 OD1    -0.173    2.878
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A LEU 2058 CD1   /A ARG 2059 N      -0.181    3.506
    /A ILE 2025 H     /A ASN 2024 CG     -0.182    2.882
    /A ILE 2060 HD11  /A LEU 2058 HD21   -0.184    2.184
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A ILE 2079 HA    /A ARG 2059 O      -0.193    2.673
    /A GLU 2021 HG3   /A LEU 2020 C      -0.201    2.901
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A LEU 2022 N     /A LEU 2058 O      -0.208    2.913
    /A LEU 2058 CD1   /A ASN 2080 O      -0.211    3.391
    /A ALA 2082 O     /A VAL 2081 CG1    -0.214    3.394
    /A LEU 2058 HD12  /A ARG 2059 N      -0.216    2.841
    /A ALA 2082 H     /A VAL 2057 C      -0.217    2.917
    /A ARG 2059 H     /A LEU 2058 HD12   -0.233    2.233
    /A VAL 2081 HG21  /A ASN 2080 C      -0.237    2.937
    /A LEU 2020 O     /A LEU 2020 HD21   -0.248    2.728
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2060 H     /A LEU 2020 C      -0.254    2.954
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A VAL 2081 CG2   /A LEU 2058 CD1    -0.259    3.659
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2058 H     /A LEU 2022 O      -0.267    2.347
    /A ASN 2080 H     /A ARG 2059 C      -0.271    2.971
    /A VAL 2081 CA    /A VAL 2057 O      -0.276    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.277    3.457
    /A LEU 2058 HD21  /A ILE 2060 CD1    -0.280    2.980
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A LEU 2058 O     /A GLU 2021 CA     -0.282    3.462
    /A THR 2085 H     /A LEU 2041 C      -0.283    2.983
    /A ASN 2080 O     /A LEU 2058 CA     -0.284    3.464
    /A ILE 2079 HG22  /A LEU 2058 HD11   -0.300    2.300
    /A LEU 2058 HB2   /A LEU 2022 CB     -0.304    3.004
    /A LEU 2020 H     /A ILE 2060 C      -0.314    3.014
    /A ILE 2084 C     /A LEU 2041 O      -0.315    3.495
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A ILE 2060 HG13  /A ARG 2059 C      -0.333    3.033
    /A GLU 2021 CG    /A LEU 2020 O      -0.333    3.513
    /A ARG 2059 H     /A ASN 2080 C      -0.333    3.033
    /A ARG 2059 C     /A LEU 2020 O      -0.340    3.520
    /A LEU 2020 CD2   /A LEU 2020 O      -0.340    3.520
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A ILE 2084 HG22  /A ALA 2082 C      -0.348    3.048
    /A LEU 2058 CB    /A LEU 2022 HB3    -0.353    3.053
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ILE 2084 CB    /A LEU 2041 O      -0.357    3.537
    /A THR 2085 O     /A LEU 2041 N      -0.358    3.063
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A VAL 2057 CB    /A GLY 2023 O      -0.369    3.549
    /A LEU 2022 HG    /A ASN 2024 O      -0.372    2.852
    /A VAL 2057 CG2   /A GLY 2023 C      -0.375    3.775
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A LEU 2058 HD11  /A ILE 2079 CG2    -0.378    3.078
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A ILE 2079 CA    /A ARG 2059 O      -0.394    3.574
    /A ASN 2024 O     /A LEU 2022 CG     -0.396    3.576
    

  
134 contacts  

> ui tool show Clashes

> clashes sel saveFile C:/Users/emirm/Desktop/contacts/l2058_cla_file restrict
> both intraRes true ignoreHiddenModels true select true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> hide #1.3 models

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 134 pseudobonds, 20 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/emirm/Desktop/contacts/l2058_hbond_file color
> #00ff00 dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    10 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N  /A ILE 2060 O  /A LEU 2020 H  2.857  1.850
    /A LEU 2022 N  /A LEU 2058 O  /A LEU 2022 H  2.913  2.002
    /A LEU 2041 N  /A THR 2085 O  /A LEU 2041 H  3.063  2.100
    /A VAL 2057 N  /A LEU 2022 O  /A VAL 2057 H  2.815  2.059
    /A LEU 2058 N  /A LEU 2022 O  /A LEU 2058 H  3.346  2.347
    /A ARG 2059 N  /A ASN 2080 O  /A ARG 2059 H  2.872  1.872
    /A ILE 2060 N  /A LEU 2020 O  /A ILE 2060 H  2.817  1.825
    /A ASN 2080 N  /A ARG 2059 O  /A ASN 2080 H  2.752  1.762
    /A ALA 2082 N  /A VAL 2057 O  /A ALA 2082 H  2.859  1.852
    /A THR 2085 N  /A LEU 2041 O  /A THR 2085 H  2.749  1.790
    

  
10 hydrogen bonds found  

> hide #1.4 models

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/session_L2058.cxs

[Repeated 1 time(s)]

> ui windowfill toggle

[Repeated 1 time(s)]

> save C:/Users/emirm/Desktop/contacts/l2058_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.2 models

> show #1.3 models

> select subtract #1.3

Nothing selected  

> hide #1.3 models

> show #1.3 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.3 models

> show #1.4 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_hb.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.4 models

> close #1.2-4

> select /A:2058

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

> select /A:2058

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

> color (#!1 & sel) orange red

> color (#!1 & sel) orange

> select /A:2081

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:2081

16 atoms, 15 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) red

> select /A:2147

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

> select /A:2147

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

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> show sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select add /A:2187

354 atoms, 350 bonds, 21 residues, 2 models selected  

> select add /A:2186

370 atoms, 365 bonds, 22 residues, 2 models selected  

> select add /A:2185

384 atoms, 379 bonds, 23 residues, 2 models selected  

> select add /A:2184

400 atoms, 394 bonds, 24 residues, 2 models selected  

> select subtract /A:2184

384 atoms, 379 bonds, 23 residues, 2 models selected  

> select add /A:2184

400 atoms, 394 bonds, 24 residues, 2 models selected  

> select add /A:2183

415 atoms, 408 bonds, 25 residues, 2 models selected  

> select add /A:2181

434 atoms, 426 bonds, 26 residues, 2 models selected  

> select add /A:2182

448 atoms, 440 bonds, 27 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select subtract /A:2020

429 atoms, 421 bonds, 26 residues, 2 models selected  

> select subtract /A:2021

414 atoms, 406 bonds, 25 residues, 2 models selected  

> select subtract /A:2022

395 atoms, 387 bonds, 24 residues, 2 models selected  

> select subtract /A:2023

388 atoms, 380 bonds, 23 residues, 2 models selected  

> select subtract /A:2024

374 atoms, 366 bonds, 22 residues, 2 models selected  

> select subtract /A:2025

355 atoms, 347 bonds, 21 residues, 2 models selected  

> select subtract /A:2042

345 atoms, 337 bonds, 20 residues, 2 models selected  

> select subtract /A:2041

326 atoms, 319 bonds, 19 residues, 2 models selected  

> select subtract /A:2026

302 atoms, 296 bonds, 18 residues, 2 models selected  

> select add /A:2041

321 atoms, 314 bonds, 19 residues, 2 models selected  

> select add /A:2042

331 atoms, 323 bonds, 20 residues, 2 models selected  

> select add /A:2040

350 atoms, 341 bonds, 21 residues, 2 models selected  

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> select /A:2237

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

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> select /A:2237-2238

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> save C:/Users/emirm/Desktop/contacts/session_V2081.cxs

——— End of log from Wed Jul 30 09:34:05 2025 ———

> view name session-start

opened ChimeraX session  

> select /A:2260

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:2260-2261

28 atoms, 28 bonds, 2 residues, 1 model selected  

> ui windowfill toggle

> ui mousemode right translate

> save C:/Users/emirm/Desktop/contacts/v2081_zoomedout.tif width 1280 height
> 491 supersample 3

> ui mousemode right select

Drag select of 262 residues  

> show sel surfaces

> transparency (#!1 & sel) 70

> select clear

> save C:/Users/emirm/Desktop/contacts/v2081_zoomedoutsurface.tif width 1280
> height 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
386892 of 3435358 triangles, 262 residues  

> hide sel surfaces

> select clear

> ui windowfill toggle

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> ui windowfill toggle

> ui mousemode right translate

> ui windowfill toggle

> show sel atoms

> hide sel cartoons

> ui tool show Contacts


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

Log:
UCSF ChimeraX version: 1.10.dev202503131841 (2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\contacts\\\session_V2081.cxs

Log from Wed Jul 30 09:34:05 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\contacts\\\session_L2058.cxs

Log from Wed Jul 30 08:19:51 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\contacts\\\Contacts.cxs

Log from Tue Jul 29 15:17:34 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\emirm\\\Desktop\\\Fly\\\Chimera_WorkingFolder\\\Contacts_Modeling_Chimera\\\Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

Log from Fri Jul 25 15:41:25 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\emirm\\\Desktop\\\Fly\\\Chimera_WorkingFolder\\\Contacts_Modeling_Chimera\\\Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

Log from Fri May 2 10:11:43 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\emirm\\\Desktop\\\Fly\\\Chimera_WorkingFolder\\\Contacts_Modeling_Chimera\\\Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

Log from Wed Apr 30 15:52:46 2025UCSF ChimeraX version: 1.10.dev202503131841
(2025-03-13)  
© 2016-2025 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\emirm\\\Desktop\\\Fly\\\AlphaFold\\\Chimera\\\Apt1.cxs

Log from Fri Mar 7 14:18:08 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:\Users\emirm\Desktop\Fly\AlphaFold\Superpositions_hob.cxs format
> session

Log from Thu Mar 6 15:37:27 2025UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

Log from Mon Mar 3 14:52:27 2025 Startup Messages  
---  
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  

> open
> C:/Users/emirm/Downloads/fold_2025_02_26_14_57_hob_native/fold_2025_02_26_14_57_hob_native_model_0.cif

Chain information for fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
Chain | Description  
A | .  
  
Computing secondary structure  
No Surface models open  

> select add #1

18469 atoms, 18843 bonds, 2300 residues, 1 model selected  
No Surface models open  

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface style mesh

> select subtract #1

1 model selected  

> surface style dot

> color #1 cyan

> color #1 #aaff00ff

> mlp

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface style mesh

> transparency 50

> surface style solid

> color #1 red

> mlp

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> transparency 50

> surface style mesh

> cartoon style modeHelix tube sides 20

> color #1 yellow

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface #1.1: minimum, -16.90, mean -0.15, maximum 17.22  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 70

> open
> C:/Users/emirm/Downloads/fold_2025_03_03_10_24_hob_helicalcaptop/fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif

Chain information for fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2  
---  
Chain | Description  
A | .  
  
Computing secondary structure  

> hide #!1 models

> mlp #2

Map values for surface "fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif_A
SES surface": minimum -29.41, mean -3.659, maximum 24.89  
To also show corresponding color key, enter the above mlp command and add key
true  

> surface style #2 mesh

> transparency #2 70

> show #!1 models

> hide #!1 models

> show #!1 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

> mmaker #2 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_2025_02_26_14_57_hob_native_model_0.cif, chain A (#1) with
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif, chain A (#2), sequence
alignment score = 11457.7  
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:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 1  
RMSD between 1351 pruned atom pairs is 0.823 angstroms; (across all 2271
pairs: 20.273)  
  

> surface hidePatches

> hide #!1 models

> cartoon style #2 modeHelix tube sides 20

> show #!1 models

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\emirm/Desktop\movie2.mp4

Movie saved to C:\Users\emirm/Desktop\movie2.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode C:\Users\emirm/Desktop\movie3.mp4

Movie saved to C:\Users\emirm/Desktop\movie3.mp4  
  

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> surface

> transparency 30

> surface hidePatches

> open
> C:/Users/emirm/Downloads/fold_2025_03_03_11_19_hob_l2221p/fold_2025_03_03_11_19_hob_l2221p_model_0.cif

Chain information for fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3  
---  
Chain | Description  
A | .  
  
Associated fold_2025_03_03_11_19_hob_l2221p_model_0.cif chain A to
fold_2025_02_26_14_57_hob_native_model_0.cif, chain A with 1 mismatch  
Chains used in RMSD evaluation for alignment 1:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A  
Computing secondary structure  

> hide #!2 models

> mmaker #3 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_2025_02_26_14_57_hob_native_model_0.cif, chain A (#1) with
fold_2025_03_03_11_19_hob_l2221p_model_0.cif, chain A (#3), sequence alignment
score = 11719.1  
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:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 2  
RMSD between 1478 pruned atom pairs is 1.025 angstroms; (across all 2300
pairs: 4.757)  
  

> hide #!1 models

> cartoon style #3 modeHelix tube sides 20

> show #!1 models

> hide #3 models

> open
> C:/Users/emirm/Downloads/fold_2025_03_03_11_19_hob_l2221ppppp/fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif

Chain information for fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4  
---  
Chain | Description  
A | .  
  
Associated fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif chain A to
fold_2025_02_26_14_57_hob_native_model_0.cif, chain A with 5 mismatches  
Chains used in RMSD evaluation for alignment 1:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A,
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A  
Associated fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif chain A to
fold_2025_03_03_11_19_hob_l2221p_model_0.cif, chain A with 4 mismatches  
Chains used in RMSD evaluation for alignment 2:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A,
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A  
Computing secondary structure  

> hide #!1 models

> cartoon style #4 modeHelix tube sides 20

> show #!1 models

> mmaker #4 to #1 showAlignment true

Computing secondary structure  
[Repeated 1 time(s)]  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 fold_2025_02_26_14_57_hob_native_model_0.cif, chain A (#1) with
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif, chain A (#4), sequence
alignment score = 11678.5  
Alignment identifier is 3  
Showing conservation header ("seq_conservation" residue attribute) for
alignment 3  
Hiding conservation header for alignment 3  
Chains used in RMSD evaluation for alignment 3:
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A,
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A  
Showing rmsd header ("seq_rmsd" residue attribute) for alignment 3  
RMSD between 1213 pruned atom pairs is 0.897 angstroms; (across all 2300
pairs: 10.567)  
  

> show #!2 models

> hide #!2 models

> show #3 models

> hide #3 models

> surface #1,4

> surface hidePatches #1,4

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

——— End of log from Mon Mar 3 14:52:27 2025 ———

opened ChimeraX session  

> hide #!4 models

> color #1 #ffff7fff

> show #!2 models

> hide #!2 models

Alignment identifier is 1/A  
Alignment identifier is 2/A  
Alignment identifier is 3/A  
Alignment identifier is 4/A  

> select #1/A:102

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:102-115

118 atoms, 118 bonds, 14 residues, 1 model selected  

> select #1/A:1972

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:1972-2080

886 atoms, 899 bonds, 109 residues, 1 model selected  

> select #1/A:1972-2089

948 atoms, 962 bonds, 118 residues, 1 model selected  

> color (#!1 & sel) orange

> show sel atoms

> style sel ball

Changed 948 atom styles  

> hide sel atoms

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #1/A:2058

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #1/A:2080

23 atoms, 20 bonds, 3 residues, 2 models selected  

> select add #1/A:2059

34 atoms, 30 bonds, 4 residues, 2 models selected  

> select add #1/A:2057

41 atoms, 36 bonds, 5 residues, 2 models selected  

> select add #1/A:2082

46 atoms, 40 bonds, 6 residues, 2 models selected  

> select add #1/A:2021

55 atoms, 48 bonds, 7 residues, 2 models selected  

> select add #1/A:2022

63 atoms, 55 bonds, 8 residues, 2 models selected  

> select add #1/A:2023

67 atoms, 58 bonds, 9 residues, 2 models selected  

> select add #1/A:2056

78 atoms, 68 bonds, 10 residues, 2 models selected  

> show sel atoms

> color bfactor sel

78 atoms, 10 residues, 1 surfaces, atom bfactor range 42.9 to 88.1  

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

78 atoms, 10 residues, 1 surfaces, atom bfactor range 42.9 to 88.1  

> color bfactor sel

78 atoms, 10 residues, 1 surfaces, atom bfactor range 42.9 to 88.1  

> hide sel surfaces

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> ui tool show Contacts

Restriction atom specifier must not be blank  

> contacts sel saveFile C:/Users/emirm/Desktop/Contacts_trial restrict both
> intraRes true ignoreHiddenModels true select true color #6a6a6a dashes 5
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    36 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.731    2.789
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.496    2.994
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.469    2.561
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   0.445    2.215
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.084    2.946
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.067    3.453
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    0.039    3.721
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.025    3.495
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2   -0.046    2.706
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.178    3.478
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   -0.211    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CB    -0.284    4.044
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.318    3.618
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE    -0.359    3.019
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    -0.391    4.151
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
36 contacts  

> contacts sel saveFile C:/Users/emirm/Desktop/Contacts_trial2 restrict both
> intraRes true ignoreHiddenModels true select true color #6a6a6a dashes 5
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    36 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.731    2.789
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.496    2.994
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.469    2.561
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   0.445    2.215
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CZ    0.084    2.946
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.067    3.453
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    0.039    3.721
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CD    0.025    3.495
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH2   -0.046    2.706
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.178    3.478
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NH1   -0.211    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CB    -0.284    4.044
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.318    3.618
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 OE2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 NE    -0.359    3.019
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2056 CD    -0.391    4.151
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
36 contacts  

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/emirm/Desktop/H-bonds_trial dashes 4 restrict
> both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    5 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
5 hydrogen bonds found  

> hbonds sel saveFile C:/Users/emirm/Desktop/H-bonds_trial2 dashes 4 restrict
> both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    5 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
5 hydrogen bonds found  

> hide #1.2 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Superpositions_hob.cxs

——— End of log from Thu Mar 6 15:37:27 2025 ———

opened ChimeraX session  

> select #2/A:16-17

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #2/A:16-17

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #1/A:2056

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

> select #1/A:2056-2102

379 atoms, 388 bonds, 17 pseudobonds, 47 residues, 3 models selected  

> select #1/A:2055

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

> select #1/A:1961-2055

766 atoms, 775 bonds, 95 residues, 1 model selected  

> color (#!1 & sel) #ffff7fff

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6684 atoms, 6718 bonds, 15 pseudobonds, 812 residues, 3 models selected  

> select #1/A:2056

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

> select #1/A:2056-2102

379 atoms, 388 bonds, 17 pseudobonds, 47 residues, 3 models selected  

> color (#!1 & sel) orange

> select #1/A:2055

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

> select #1/A:1990-2055

525 atoms, 531 bonds, 66 residues, 1 model selected  

> color #1 white

> color #1 #8b8b8bff

> color #1 #cfcfcfff

> select #1/A:2056

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

> select #1/A:2056-2102

379 atoms, 388 bonds, 17 pseudobonds, 47 residues, 3 models selected  

> color (#!1 & sel) orange

> select #1/A:2042

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select #1/A:2020-2042

191 atoms, 192 bonds, 23 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> select #1/A:2176

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

> select #1/A:2176-2194

159 atoms, 163 bonds, 19 residues, 1 model selected  

> color (#!1 & sel) hot pink

> select #1/A:2198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2198-2238

343 atoms, 351 bonds, 41 residues, 1 model selected  

> color (#!1 & sel) purple

> hide #1.3 models

> select subtract #1.1

1 model selected  

> hide #1.1 models

> select add #1.1

18469 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> select #1/A:2198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2198-2238

343 atoms, 351 bonds, 41 residues, 1 model selected  

> color (#!1 & sel) lime

> select subtract #1.1

1 model selected  

> select add #1

18469 atoms, 18843 bonds, 41 pseudobonds, 2300 residues, 3 models selected  

> hide sel atoms

> hide #!1 models

> show #!1 models

> select subtract #1.1

1 model selected  

> select add #1.2

36 pseudobonds, 1 model selected  

> save C:\Users\emirm/Desktop\image1.png supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole.png width 816 height
> 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole.tif width 816 height
> 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole_180.tif width 816
> height 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Whole.tif width 816 height
> 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1.tif width 816 height
> 443 supersample 3

> select add #1/A:2020

8 atoms, 7 bonds, 36 pseudobonds, 1 residue, 2 models selected  

> select add #1/A:2021

17 atoms, 15 bonds, 36 pseudobonds, 2 residues, 3 models selected  

> select add #1/A:2022

25 atoms, 22 bonds, 36 pseudobonds, 3 residues, 3 models selected  

> select add #1/A:2060

33 atoms, 29 bonds, 36 pseudobonds, 4 residues, 3 models selected  

> select add #1/A:2059

44 atoms, 39 bonds, 36 pseudobonds, 5 residues, 3 models selected  

> select add #1/A:2058

52 atoms, 46 bonds, 36 pseudobonds, 6 residues, 3 models selected  

> select add #1/A:2078

61 atoms, 54 bonds, 36 pseudobonds, 7 residues, 3 models selected  

> select add #1/A:2079

69 atoms, 61 bonds, 36 pseudobonds, 8 residues, 3 models selected  

> select add #1/A:2080

77 atoms, 68 bonds, 36 pseudobonds, 9 residues, 3 models selected  

> select add #1/A:2081

84 atoms, 74 bonds, 36 pseudobonds, 10 residues, 3 models selected  

> select subtract #1/A:2078

75 atoms, 66 bonds, 36 pseudobonds, 9 residues, 3 models selected  

> select add #1/A:2082

80 atoms, 70 bonds, 36 pseudobonds, 10 residues, 3 models selected  

> select add #1/A:2056

91 atoms, 80 bonds, 36 pseudobonds, 11 residues, 3 models selected  

> select add #1/A:2023

95 atoms, 83 bonds, 36 pseudobonds, 12 residues, 3 models selected  

> select add #1/A:2057

102 atoms, 89 bonds, 36 pseudobonds, 13 residues, 3 models selected  

> select subtract #1/A:2056

91 atoms, 79 bonds, 21 pseudobonds, 12 residues, 3 models selected  

> show sel atoms

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor sel

91 atoms, 12 residues, 1 surfaces, atom bfactor range 51.2 to 89.1  

> hide sel surfaces

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> hide sel surfaces

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues.tif width
> 816 height 443 supersample 3

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_contacts restrict both
> intraRes true ignoreHiddenModels true select true color #6a6a6a dashes 4
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    31 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     0.034    3.266
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2   -0.044    3.804
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2   -0.059    3.579
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.157    2.817
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.189    3.949
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N     -0.197    2.857
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.213    3.513
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.220    3.520
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.274    3.574
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 CG1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.376    4.136
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
31 contacts  

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_contacts2 restrict
> both intraRes true ignoreHiddenModels true select true color #6a6a6a dashes
> 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    31 contacts
                                atom1                                                           atom2                               overlap  distance
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2   0.429    2.871
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   0.046    3.714
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     0.034    3.266
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2   -0.044    3.804
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2   -0.059    3.579
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CA    -0.060    3.820
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.092    2.752
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG1   -0.094    3.394
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O     -0.155    2.815
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.156    3.456
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.157    2.817
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CA    -0.162    3.462
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CA    -0.164    3.464
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.189    3.949
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N     -0.197    2.857
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O     -0.199    2.859
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.212    2.872
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLU 2021 CG   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.213    3.513
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 CD2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O     -0.220    3.520
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 O     -0.249    3.549
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O     -0.253    2.913
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2079 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.274    3.574
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A GLY 2023 C     -0.285    3.775
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CA   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.303    3.603
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 CB    -0.309    4.069
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.326    3.846
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 CB    -0.342    3.642
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 CG1  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 CD1   -0.376    4.136
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2081 CG2  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O     -0.380    3.680
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB    -0.387    4.147
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 CB   fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O     -0.399    3.699
    

  
31 contacts  

> show #1.2 models

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_contacts.tif
> width 816 height 443 supersample 3

> show #1.3 models

> hide #1.3 models

> close #1.3

> ui tool show Distances

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_h-
> bonds dashes 4 restrict both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    7 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O  no hydrogen  2.857  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O  no hydrogen  2.817  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
7 hydrogen bonds found  

> hbonds sel saveFile C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_h-
> bonds2 dashes 4 restrict both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    7 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O  no hydrogen  2.857  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O  no hydrogen  2.817  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
7 hydrogen bonds found  

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_h-bonds.tif
> width 778 height 443 supersample 3

> hide #1.3 models

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_clashes restrict both
> ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: False
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/residues_clashes2 restrict both
> ignoreHiddenModels true reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: False
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> hide #1.4 models

> show #1.4 models

> select subtract #1.4

39 atoms, 12 residues, 2 models selected  

> hide #1.4 models

> select subtract #1.4

39 atoms, 12 residues, 2 models selected  

> show #1.4 models

> hide #1.4 models

> select subtract #1.4

39 atoms, 12 residues, 2 models selected  

> ui tool show Angles/Torsions

> ui tool show "Check Waters"

QWindowsWindow::setMouseGrabEnabled: Not setting mouse grab for invisible
window QWidgetWindow/'QMenuClassWindow'  

[Repeated 4 time(s)]

> hbonds interModel false reveal true restrict any name "water H-bonds"

7487 hydrogen bonds found  

> ~select

Nothing selected  

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> show #1.5 models

> select add #1.5

1868 pseudobonds, 1 model selected  

> hide #1.5 models

> show #1.5 models

> select subtract #1.5

Nothing selected  

> hide #1.5 models

> hide #!1 atoms

> select add #1.1

18469 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> select add #1.2

31 pseudobonds, 1 model selected  

> select subtract #1.2

Nothing selected  

> select add #1.2

31 pseudobonds, 1 model selected  

> select subtract #1.2

Nothing selected  

> show #1.2 models

> select add #1.2

31 pseudobonds, 1 model selected  

> show #!1 atoms

[Repeated 1 time(s)]

> hide #!1 atoms

> hide #1.2 models

> select subtract #1.2

Nothing selected  

> select subtract #1.4

Nothing selected  

> select #1/A:2020

8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/A:2020-2023

29 atoms, 28 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2020-2023,2057-2060

63 atoms, 61 bonds, 24 pseudobonds, 8 residues, 4 models selected  

> select #1/A:2020-2023,2057-2060,2079-2082

91 atoms, 88 bonds, 46 pseudobonds, 12 residues, 4 models selected  

> style sel ball

Changed 91 atom styles  

> show sel atoms

> select subtract #1.1

1 model selected  

> select add #1.2

31 pseudobonds, 1 model selected  

> select add #1.3

38 pseudobonds, 2 models selected  

> select subtract #1.4

38 pseudobonds, 2 models selected  

> select subtract #1.3

31 pseudobonds, 1 model selected  

> select subtract #1.2

Nothing selected  

> select subtract #1.4

Nothing selected  

> show #1.2 models

> log metadata #1

No models had metadata

> log chains #1

Chain information for fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> select add #1.2

31 pseudobonds, 1 model selected  

> log metadata #1

No models had metadata

> log chains #1

Chain information for fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
Chain | Description  
A | .  
  

> interfaces #!1 & ~solvent

0 buried areas:  

> ui tool show Contacts

> help help:user/tools/clashes.html

> select subtract #1.2

Nothing selected  

> select subtract #1.4

Nothing selected  

> hide #1.2 models

> select #1/A:2055

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

> select add #1/A:2054

19 atoms, 18 bonds, 2 residues, 2 models selected  

> hide sel cartoons

> select #1/A:1618

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

> select #1/A:1619

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select #1/A:1618

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

> select add #1/A:1619

15 atoms, 13 bonds, 2 residues, 2 models selected  

> select add #1/A:1620

26 atoms, 23 bonds, 3 residues, 2 models selected  

> hide sel cartoons

> select add #1/A:1617

33 atoms, 29 bonds, 4 residues, 2 models selected  

> select add #1/A:1615

43 atoms, 39 bonds, 5 residues, 2 models selected  

> select add #1/A:1616

49 atoms, 44 bonds, 6 residues, 2 models selected  

> hide sel cartoons

> select add #1/A:2053

56 atoms, 50 bonds, 7 residues, 2 models selected  

> select add #1/A:2052

64 atoms, 57 bonds, 8 residues, 2 models selected  

> hide sel cartoons

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues.tif width
> 778 height 443 supersample 3

> show #1.2 models

> select add #1/A:2056

75 atoms, 67 bonds, 9 residues, 2 models selected  

> hide sel cartoons

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues.tif width
> 778 height 443 supersample 3

> show #1.2 models

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_contacts.tif
> width 778 height 443 supersample 3

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.3 models

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_h-bonds.tif
> width 778 height 443 supersample 3

> show #1.2 models

> hide #1.2 models

> hide #1.3 models

> color #1.4 yellow models

> show #1.4 models

> hide #1.4 models

> show #1.5 models

> hide #1.5 models

> select subtract #1.4

75 atoms, 67 bonds, 9 residues, 2 models selected  

> select #1/A:2020

8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/A:2020-2023

29 atoms, 28 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2057-2058

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #1/A:2057-2060

34 atoms, 33 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2020-2023,2057-2060

63 atoms, 61 bonds, 24 pseudobonds, 8 residues, 4 models selected  

> select #1/A:2020-2023,2057-2060,2079-2082

91 atoms, 88 bonds, 46 pseudobonds, 12 residues, 4 models selected  

> coulombic sel

Coulombic values for fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface #1.1: minimum, -16.90, mean -0.15, maximum 17.22  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> mlp sel

Map values for surface "fold_2025_02_26_14_57_hob_native_model_0.cif_A SES
surface": minimum -29.39, mean -3.629, maximum 25.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> save C:\Users\emirm/Desktop\image2.png supersample 3

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_hydrophobicity.tif
> width 778 height 443 supersample 3

> volume style mesh

No volumes specified  

> surface style #1 mesh

> surface (#!1 & sel)

> transparency (#!1 & sel) 50

> select subtract #1.1

1 model selected  

> select add #1.1

18469 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> transparency #1.1#!1 20

> transparency #1.1#!1 0

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom2_residues_hydrophobicity_mesh.tif
> width 778 height 443 supersample 3

> ui tool show "Color Actions"

> color byhetero

> color byelement

> color byhetero

[Repeated 1 time(s)]

> color bynucleotide

> color bychain

> undo

[Repeated 6 time(s)]

> redo

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

> ui tool show "Color Actions"

> toolshed show

Downloading bundle ChimeraX_ISOLDE-1.9-cp311-cp311-win_amd64.whl  
Downloading bundle SEQCROW-1.8.18-py3-none-any.whl  
Installed SEQCROW (1.8.18)  

> select #1/A:2059

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

> select #1/A:2059

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

> help help:user/tools/sequenceviewer.html#copy

> toolshed show

> help help:quickstart

> help help:user

> swapaa /L:2058 pro

No amino acid residues specified for swapping  

> swapaa /L:2058P

Missing or invalid "resTypes" argument: Expected a text string  

> ui tool show Rotamers

[Repeated 1 time(s)]

> swapaa interactive sel ARG rotLib Dunbrack

fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059: phi -132.9, psi
123.6 trans  
Changed 600 bond radii  

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6684 atoms, 6718 bonds, 825 pseudobonds, 812 residues, 4 models selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Rotamers

> swapaa interactive sel LEU rotLib Dunbrack

fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058: phi -137.9, psi
132.6 trans  
Changed 45 bond radii  

> hbonds #!1 & ~#!1/A:2058 & ~solvent reveal true restrict #1.6 & ~@c,ca,n

0 hydrogen bonds found  

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6684 atoms, 6718 bonds, 820 pseudobonds, 812 residues, 3 models selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> swapaa

Missing or invalid "residues" argument: empty atom specifier  

> redo

> select #1/A:2020-2023,2057-2060,2079-2082

91 atoms, 88 bonds, 39 pseudobonds, 12 residues, 3 models selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> swapaa /A:2058 leu to A:2058 val

Expected ',' or a keyword  

> swapaa /A:2058 leu A:2058 val

Expected ',' or a keyword  

> swapaa /A:L2058V

Missing or invalid "resTypes" argument: Expected a text string  

> swapaa /A:2058 val

Using Dunbrack library  
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2058: phi -137.9, psi
132.6 trans  
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A LEU 2058: phi -139.1,
psi 132.6 trans  
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A LEU 2058: phi -138.8, psi
132.1 trans  
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A LEU 2058: phi -136.2,
psi 130.5 trans  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2058  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A VAL 2058  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A VAL 2058  
Applying VAL rotamer (chi angles: 179.2) to
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A VAL 2058  

> select
> #1/A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6683 atoms, 6717 bonds, 815 pseudobonds, 812 residues, 3 models selected  

> swapaa /A:2058 pro

Using Dunbrack library  
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2058: phi -137.9, psi
132.6 trans  
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A VAL 2058: phi -139.1,
psi 132.6 trans  
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A VAL 2058: phi -138.8, psi
132.1 trans  
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A VAL 2058: phi -136.2,
psi 130.5 trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to
fold_2025_02_26_14_57_hob_native_model_0.cif #1/A PRO 2058  
Applying PRO rotamer (chi angles: 27.3 -34.5) to
fold_2025_03_03_10_24_hob_helicalcaptop_model_0.cif #2/A PRO 2058  
Applying PRO rotamer (chi angles: 27.3 -34.5) to
fold_2025_03_03_11_19_hob_l2221p_model_0.cif #3/A PRO 2058  
Applying PRO rotamer (chi angles: -25.1 36.3) to
fold_2025_03_03_11_19_hob_l2221ppppp_model_0.cif #4/A PRO 2058  

> select
> #1/A:2-32,134-142,212-214,256-268,291-300,402-420,458-463,513-519,588-605,696-698,737-756,841-849,878-896,929-965,971-998,1022-1024,1027-1037,1142-1144,1146-1158,1171-1178,1275-1277,1325-1339,1349-1351,1361-1363,1490-1497,1515-1538,1595-1604,1618-1623,1625-1631,1712-1714,1720-1722,1737-1739,1793-1795,1834-1848,1853-1871,1874-1911,1916-1958,2090-2100,2111-2113,2162-2172,2220-2247,2262-2271

4475 atoms, 4510 bonds, 460 pseudobonds, 539 residues, 2 models selected  

> select #1/A:2020

8 atoms, 7 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select #1/A:2020-2023

29 atoms, 28 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:2057-2060

33 atoms, 33 bonds, 4 residues, 1 model selected  

> select #1/A:2078-2079

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #1/A:2078-2082

37 atoms, 36 bonds, 4 pseudobonds, 5 residues, 3 models selected  

> select #1/A:2079

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #1/A:2079-2082

28 atoms, 27 bonds, 3 pseudobonds, 4 residues, 2 models selected  

> select #1/A:2057-2060,2079-2082

61 atoms, 60 bonds, 17 pseudobonds, 8 residues, 3 models selected  

> select #1/A:2020-2023,2057-2060,2079-2082

90 atoms, 88 bonds, 34 pseudobonds, 12 residues, 3 models selected  

> hide sel surfaces

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_L2058P.tif
> width 778 height 443 supersample 3

> select subtract #1.1

3 atoms, 2 bonds, 1 residue, 2 models selected  

> select subtract #1.4

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

> show #1.2 models

> save
> C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_L2058P_contacts.tif
> width 778 height 443 supersample 3

> show #1.5 models

> hide #1.2 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> show #1.5 models

> hide #1.5 models

> select add #1.5

3 atoms, 2 bonds, 1868 pseudobonds, 1 residue, 2 models selected  

> select subtract #1.5

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

> show #1.5 models

> hide #1.5 models

> show #1.4 models

> select subtract #1.4

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

> hide #1.4 models

> show #1.2 models

> hide #1.2 models

> show #1.5 models

> hide #1.5 models

> close #1.5

> select #1/A:2020-2023,2057-2060,2079-2082

90 atoms, 88 bonds, 26 pseudobonds, 12 residues, 2 models selected  

> select #1/A:2020-2023,2057-2061,2079-2082

101 atoms, 100 bonds, 26 pseudobonds, 13 residues, 2 models selected  

> select #1/A:2020-2023,2057-2061,2079-2082

101 atoms, 100 bonds, 26 pseudobonds, 13 residues, 2 models selected  

> select #1/A:2020-2023,2057-2061,2079-2082

101 atoms, 100 bonds, 26 pseudobonds, 13 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel dashes 4 restrict both reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    7 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 O  no hydrogen  2.857  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A PRO 2058 O  no hydrogen  2.913  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2022 O  no hydrogen  2.815  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 O  no hydrogen  2.872  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ILE 2060 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A LEU 2020 O  no hydrogen  2.817  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ASN 2080 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ARG 2059 O  no hydrogen  2.752  N/A
    fold_2025_02_26_14_57_hob_native_model_0.cif #1/A ALA 2082 N  fold_2025_02_26_14_57_hob_native_model_0.cif #1/A VAL 2057 O  no hydrogen  2.859  N/A
    

  
7 hydrogen bonds found  

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Zoom1_residues_L2058P_h-
> bonds.tif width 778 height 443 supersample 3

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

> show #!2 models

> show #!3 models

> close #2-4

> save C:/Users/emirm/Desktop/Fly/AlphaFold/Chimera/Apt1.cxs

[Repeated 1 time(s)]

——— End of log from Fri Mar 7 14:18:08 2025 ———

> view name session-start

opened ChimeraX session  

> select
> /A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6683 atoms, 6718 bonds, 22 pseudobonds, 812 residues, 3 models selected  

> select /A:2151-2152

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:2151-2152

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select
> /A:2-32,134-142,212-214,256-268,291-300,402-420,458-463,513-519,588-605,696-698,737-756,841-849,878-896,929-965,971-998,1022-1024,1027-1037,1142-1144,1146-1158,1171-1178,1275-1277,1325-1339,1349-1351,1361-1363,1490-1497,1515-1538,1595-1604,1618-1623,1625-1631,1712-1714,1720-1722,1737-1739,1793-1795,1834-1848,1853-1871,1874-1911,1916-1958,2090-2100,2111-2113,2162-2172,2220-2247,2262-2271

4475 atoms, 4510 bonds, 539 residues, 1 model selected  

> select
> /A:35-37,40-42,47-49,51-55,58-62,64-69,80-85,87-93,143-148,150-156,162-169,171-179,184-192,194-201,218-233,240-248,251-255,304-310,312-317,325-329,331-339,351-359,361-364,369-373,375-383,386-394,396-401,467-475,477-483,486-492,494-501,524-531,533-536,557-559,561-569,572-580,582-586,637-644,646-651,657-662,664-669,673-679,681-686,701-706,708-714,722-727,731-736,774-779,782-788,794-800,802-806,810-814,816-821,824-830,832-837,860-865,867-872,913-918,920-926,1005-1012,1014-1019,1050-1062,1064-1069,1077-1080,1082-1093,1100-1108,1112-1119,1123-1133,1135-1140,1179-1187,1189-1195,1206-1212,1214-1219,1222-1234,1242-1247,1250-1260,1295-1306,1320-1324,1365-1374,1377-1382,1389-1395,1397-1409,1420-1433,1435-1442,1463-1471,1473-1479,1502-1507,1510-1513,1635-1638,1640-1645,1647-1652,1659-1664,1666-1674,1677-1679,1682-1684,1686-1694,1697-1701,1771-1775,1780-1787,1819-1825,1827-1832,1972-1980,1982-1988,1995-2002,2004-2011,2016-2022,2024-2029,2038-2042,2058-2065,2072-2081,2084-2089,2174-2176,2178-2181,2184-2191,2204-2208,2211-2214,2216-2218

6683 atoms, 6718 bonds, 22 pseudobonds, 812 residues, 3 models selected  

> select /A:2050

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2050-2100

408 atoms, 418 bonds, 17 pseudobonds, 51 residues, 3 models selected  

> select /A:1831

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:1831-2300

3800 atoms, 3854 bonds, 33 pseudobonds, 470 residues, 3 models selected  

> show sel atoms

[Repeated 1 time(s)]

> style (#!1 & sel) stick

Changed 3800 atom styles  

> select /A:2027

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2027-2091

523 atoms, 532 bonds, 17 pseudobonds, 65 residues, 3 models selected  

> select /A:2273-2300

220 atoms, 221 bonds, 28 residues, 1 model selected  

> select /A:1711-2300

4727 atoms, 4803 bonds, 33 pseudobonds, 590 residues, 3 models selected  

> hide sel atoms

> hide #!1 models

> show #!1 models

> close #1.1-4

> select subtract /A:2020

4719 atoms, 4794 bonds, 589 residues, 1 model selected  

> select subtract /A:2021

4710 atoms, 4785 bonds, 588 residues, 1 model selected  

> select add #1

18468 atoms, 18843 bonds, 2300 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /A:2021

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select subtract /A:2021

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select add /A:2021

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select add /A:2022

25 atoms, 22 bonds, 3 residues, 1 model selected  

> select add /A:2023

29 atoms, 25 bonds, 4 residues, 1 model selected  

> color sel cornflower blue

> select /A:2159

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

> select /A:2156-2159

33 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A:2056

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

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> color sel orange

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1938

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1938

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1923

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1923-2300

3033 atoms, 3079 bonds, 378 residues, 1 model selected  

> show sel cartoons

> select /A:1787

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

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:1787-1852

524 atoms, 538 bonds, 66 residues, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2040-2102

505 atoms, 517 bonds, 63 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2040-2102

505 atoms, 517 bonds, 63 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2040

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2040-2055

127 atoms, 128 bonds, 16 residues, 1 model selected  

> select /A:2040-2055,2180-2188

199 atoms, 201 bonds, 25 residues, 1 model selected  

> select /A:2020-2026,2040-2055,2180-2188

255 atoms, 256 bonds, 32 residues, 1 model selected  

> select /A:2058

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2236

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

> select /A:2205-2236

268 atoms, 275 bonds, 32 residues, 1 model selected  

> select /A:2125

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:2125

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:2056

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

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select
> /A:2-32,134-142,212-214,256-268,291-300,402-420,458-463,513-519,588-605,696-698,737-756,841-849,878-896,929-965,971-998,1022-1024,1027-1037,1142-1144,1146-1158,1171-1178,1275-1277,1325-1339,1349-1351,1361-1363,1490-1497,1515-1538,1595-1604,1618-1623,1625-1631,1712-1714,1720-1722,1737-1739,1793-1795,1834-1848,1853-1871,1874-1911,1916-1958,2090-2100,2111-2113,2162-2172,2220-2247,2262-2271

4475 atoms, 4510 bonds, 539 residues, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2126

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2126

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2184

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2184-2187

32 atoms, 32 bonds, 4 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2021

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2020-2026

56 atoms, 55 bonds, 7 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2056-2102

378 atoms, 388 bonds, 47 residues, 1 model selected  

> select /A:2020-2027

64 atoms, 63 bonds, 8 residues, 1 model selected  

> select /A:2003-2040,2056-2102

694 atoms, 708 bonds, 85 residues, 1 model selected  

> select /A:2054-2055

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:2003-2040,2056-2102

694 atoms, 708 bonds, 85 residues, 1 model selected  

> select /A:2050-2055

48 atoms, 49 bonds, 6 residues, 1 model selected  

> select /A:2178

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

> select /A:2176-2178

31 atoms, 32 bonds, 3 residues, 1 model selected  

> select /A:2055-2056

20 atoms, 19 bonds, 2 residues, 1 model selected  

> select /A:2040-2056

138 atoms, 139 bonds, 17 residues, 1 model selected  

> select /A:2020-2028,2040-2056

211 atoms, 211 bonds, 26 residues, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2275-2300

208 atoms, 209 bonds, 26 residues, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2275-2300

208 atoms, 209 bonds, 26 residues, 1 model selected  

> select /A:2127

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2127-2157

231 atoms, 232 bonds, 31 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2020-2188

1342 atoms, 1362 bonds, 169 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2056,2180-2188

283 atoms, 284 bonds, 35 residues, 1 model selected  

> select /A:2020-2027

64 atoms, 63 bonds, 8 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2200-2201

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2200-2203

31 atoms, 30 bonds, 4 residues, 1 model selected  

> select /A:2064

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

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2064-2094

239 atoms, 244 bonds, 31 residues, 1 model selected  

> select /A:2213-2214

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

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2213-2215

30 atoms, 31 bonds, 3 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 662 bonds, 81 residues, 1 model selected  

> swapaa /A: 2058 leu

Using Dunbrack library  
/A PRO 2058: phi -137.9, psi 132.6 trans  
Applying LEU rotamer (chi angles: 177.6 65.4) to /A LEU 2058  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select /A:2300

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:2299-2300

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2300

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:2300

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

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_clashes.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    238 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.121    3.639
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A ILE 2084 CD1  /A ILE 2086 CG1   -0.021    3.781
    /A ILE 2084 CG2  /A ALA 2082 O     -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A ILE 2084 CD1  /A LEU 2040 CD1   -0.076    3.836
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A ILE 2084 CG2  /A PRO 2083 O     -0.162    3.462
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.197    3.957
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CB   /A LEU 2041 O     -0.256    3.556
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A VAL 2081 CG1  /A ILE 2084 CD1   -0.266    4.026
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.313    4.073
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A VAL 2073 CG2  /A VAL 2068 CG2   -0.328    4.088
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
238 contacts  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> hide #1.1 models

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_contacts.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> hide #1.2 models

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 291 pseudobonds, 81 residues, 4 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_hbonds.png
> width 701 height 491 supersample 3

> hide #1.3 models

> show #1.1 models

> close #1.1-3

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> hide sel atoms

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel gray

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> swapaa /A: 2068 leu

Using Dunbrack library  
/A VAL 2068: phi -108.3, psi 119.0 trans  
Applying LEU rotamer (chi angles: 177.4 64.0) to /A LEU 2068  

> ui tool show Clashes

[Repeated 1 time(s)]

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:1801-1802

14 atoms, 15 bonds, 2 residues, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_clashes.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> ui tool show Distances

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    238 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.121    3.639
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A ILE 2084 CD1  /A ILE 2086 CG1   -0.021    3.781
    /A ILE 2084 CG2  /A ALA 2082 O     -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A ILE 2084 CD1  /A LEU 2040 CD1   -0.076    3.836
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2068 CD1  /A GLY 2069 N     -0.084    3.604
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A ILE 2084 CG2  /A PRO 2083 O     -0.162    3.462
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.197    3.957
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CB   /A LEU 2041 O     -0.256    3.556
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A VAL 2081 CG1  /A ILE 2084 CD1   -0.266    4.026
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.313    4.073
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A LEU 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
238 contacts  

> hide #!1 models

> show #!1 models

> hide #1.1 models

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_contacts.png
> width 701 height 491 supersample 3

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A LEU 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A LEU 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> hide #1.2 models

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 291 pseudobonds, 81 residues, 4 models selected  

> select /A:1801

7 atoms, 7 bonds, 1 residue, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068L_hbonds.png
> width 701 height 491 supersample 3

> swapaa /A: 2068 val

Using Dunbrack library  
/A LEU 2068: phi -108.3, psi 119.0 trans  
Applying VAL rotamer (chi angles: 178.6) to /A VAL 2068  

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel gray

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel orange

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel gray

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 290 pseudobonds, 81 residues, 4 models selected  

> select /A:2071

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel orange

> swapaa /A: 2068 ile

Using Dunbrack library  
/A VAL 2068: phi -108.3, psi 119.0 trans  
Applying ILE rotamer (chi angles: -60.2 170.9) to /A ILE 2068  

> close #1.1-3

> select /A:2086

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 81 residues, 1 model selected  

> select /A:2086

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068I_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> select /A:2176

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

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> select /A:2176

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

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 5 pseudobonds, 81 residues, 2 models selected  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068I_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    239 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.121    3.639
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A ILE 2084 CD1  /A ILE 2086 CG1   -0.021    3.781
    /A ILE 2084 CG2  /A ALA 2082 O     -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A ILE 2084 CD1  /A LEU 2040 CD1   -0.076    3.836
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A ILE 2084 CG2  /A PRO 2083 O     -0.162    3.462
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.197    3.957
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CB   /A LEU 2041 O     -0.256    3.556
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A VAL 2081 CG1  /A ILE 2084 CD1   -0.266    4.026
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A ILE 2068 CD1  /A VAL 2073 CG2   -0.309    4.069
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.313    4.073
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A ILE 2068 CG1  /A VAL 2073 CG2   -0.328    4.088
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A ILE 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
239 contacts  

> select /A:2239-2240

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 244 pseudobonds, 81 residues, 3 models selected  

> select /A:2239-2240

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

652 atoms, 663 bonds, 244 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068I_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A ILE 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A ILE 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> swapaa /A: 2068 val

Using Dunbrack library  
/A ILE 2068: phi -108.3, psi 119.0 trans  
Applying VAL rotamer (chi angles: 178.6) to /A VAL 2068  

> close #1.1-3

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084-2085

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2084-2085

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084-2085

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> color sel orange

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2084

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel gray

> swapaa /A: 2084 val

Using Dunbrack library  
/A ILE 2084: phi -131.8, psi 148.9 trans  
Applying VAL rotamer (chi angles: -62.5) to /A VAL 2084  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 661 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084V_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084V_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    236 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A ALA 2082 O    /A VAL 2084 CG1   0.205    3.095
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A VAL 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A VAL 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A VAL 2186 CG1  /A VAL 2084 CG2   -0.130    3.890
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A VAL 2084 CG1  /A PRO 2083 O     -0.138    3.438
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A VAL 2084 CG2  /A ILE 2086 CG1   -0.162    3.922
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A VAL 2084 CB   /A LEU 2041 O     -0.241    3.541
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A VAL 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A VAL 2084 CG1  /A VAL 2081 CG1   -0.314    4.074
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A ILE 2086 CD1  /A VAL 2084 CG2   -0.337    4.097
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A VAL 2068 CG2  /A VAL 2073 CG2   -0.370    4.130
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
236 contacts  

> select /A:2125-2126

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 661 bonds, 241 pseudobonds, 81 residues, 3 models selected  

> select /A:2125-2126

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

650 atoms, 661 bonds, 241 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084V_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A VAL 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> close #1.1-3

> swapaa /A: 2084 leu

Using Dunbrack library  
/A VAL 2084: phi -131.8, psi 148.9 trans  
Applying LEU rotamer (chi angles: -61.3 171.4) to /A LEU 2084  

> select /A:2147

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> select /A:2147

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

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 81 residues, 1 model selected  

> ui tool show "Check Waters"

> hbonds interModel false reveal true restrict any name "water H-bonds"

1868 hydrogen bonds found  

> ~select

Nothing selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 48 pseudobonds, 81 residues, 2 models selected  

> close #1.1

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084L_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    6 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A LEU 2084 CD2  /A ALA 2042 CA    0.625    3.135
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
6 clashes  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084L_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    243 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A ALA 2042 CA   /A LEU 2084 CD2   0.625    3.135
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A LEU 2084 CD1  /A VAL 2081 CG1   0.548    3.212
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LEU 2084 CG   /A ALA 2082 O     0.215    3.085
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A LEU 2084 CD2  /A VAL 2057 CG1   0.122    3.638
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 O    /A LEU 2084 CD2   0.032    3.268
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A ALA 2042 CB   /A LEU 2084 CD2   0.023    3.737
    /A ALA 2042 N    /A LEU 2084 CD2   0.022    3.498
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A LEU 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A LEU 2041 O    /A LEU 2084 CD2   -0.060    3.360
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A LEU 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A LEU 2084 CG   /A PRO 2083 O     -0.146    3.446
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A LEU 2084 CD2  /A LEU 2041 C     -0.168    3.658
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A PRO 2083 C    /A LEU 2084 CD2   -0.219    3.709
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A LEU 2084 CB   /A LEU 2041 O     -0.236    3.536
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A LEU 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A LEU 2084 CG   /A VAL 2081 CG1   -0.300    4.060
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A VAL 2068 CG2  /A VAL 2073 CG2   -0.370    4.130
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A LEU 2084 CD1  /A ALA 2082 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
243 contacts  

> select /A:2177

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 249 pseudobonds, 81 residues, 3 models selected  

> select /A:2177

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

651 atoms, 662 bonds, 249 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084L_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A LEU 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> swapaa /A: 2084 arg

Using Dunbrack library  
/A LEU 2084: phi -131.8, psi 148.9 trans  
Applying ARG rotamer (chi angles: -64.2 -178.8 -179.3 -179.3) to /A ARG 2084  

> close #1.1-3

> select /A:2153

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> select /A:2153

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084R_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    6 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A ARG 2084 NH2  /A VAL 2057 CG1   0.633    2.887
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
6 clashes  

> select /A:2149-2150

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 6 pseudobonds, 81 residues, 2 models selected  

> select /A:2149-2151

22 atoms, 21 bonds, 3 residues, 1 model selected  

> select /A:2093

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 6 pseudobonds, 81 residues, 2 models selected  

> select /A:2093

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 6 pseudobonds, 81 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084R_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    49 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A VAL 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A VAL 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A ARG 2084 NH2  /A VAL 2057 O    no hydrogen  2.820  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ARG 2084 O    no hydrogen  2.957  N/A
    

  
49 hydrogen bonds found  

> select /A:2238

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 55 pseudobonds, 81 residues, 3 models selected  

> select /A:2238

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 55 pseudobonds, 81 residues, 3 models selected  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_I2084R_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    248 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A ARG 2084 NH2  /A VAL 2057 CG1   0.633    2.887
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2084 NH2  /A LEU 2058 CB    0.571    2.949
    /A ARG 2084 NE   /A VAL 2057 CG1   0.521    2.999
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A VAL 2081 CG1  /A ARG 2084 NE    0.437    3.083
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A ARG 2084 CD   /A VAL 2081 CG1   0.269    3.491
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A VAL 2081 CG1  /A ARG 2084 CZ    0.229    3.261
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A ARG 2084 CZ   /A VAL 2057 CG1   0.210    3.280
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A ARG 2084 CG   /A ALA 2082 O     0.148    3.152
    /A ARG 2084 NH2  /A VAL 2057 C     0.143    3.107
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A LEU 2058 CA   /A ARG 2084 NH2   0.045    3.475
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ARG 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ARG 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A LEU 2058 N    /A ARG 2084 NH2   -0.128    3.408
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A ARG 2084 CG   /A PRO 2083 O     -0.158    3.458
    /A VAL 2057 O    /A ARG 2084 NH2   -0.160    2.820
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A VAL 2081 CG1  /A ARG 2084 NH2   -0.177    3.697
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A ARG 2084 NH1  /A VAL 2081 CG1   -0.226    3.746
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A ARG 2084 CB   /A LEU 2041 O     -0.235    3.535
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A ARG 2084 NH2  /A VAL 2057 CB    -0.274    3.794
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ARG 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A ARG 2084 CZ   /A ILE 2025 CG2   -0.310    3.800
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ARG 2084 CG   /A VAL 2081 CG1   -0.355    4.115
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A VAL 2068 CG2  /A VAL 2073 CG2   -0.370    4.130
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A VAL 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
248 contacts  

> close #1.1-3

> select /A:2174

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

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> select /A:2174-2205

268 atoms, 273 bonds, 32 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

——— End of log from Wed Apr 30 15:52:46 2025 ———

> view name session-start

opened ChimeraX session  

> select add #1

18472 atoms, 18846 bonds, 2300 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

18472 atoms, 18846 bonds, 2300 residues, 1 model selected  

> hide sel atoms

> select subtract #1

Nothing selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> show sel atoms

> select subtract /A:2084

643 atoms, 653 bonds, 80 residues, 1 model selected  

> select /A:2115

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2114-2115

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

654 atoms, 665 bonds, 81 residues, 1 model selected  

> select /A:2084

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

> select /A:2084

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

> color sel orange

> swapaa /A: 2084 ile

Using Dunbrack library  
/A ARG 2084: phi -131.8, psi 148.9 trans  
Applying ILE rotamer (chi angles: 60.8 171.9) to /A ILE 2084  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068-2069

11 atoms, 10 bonds, 2 residues, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2068

7 atoms, 6 bonds, 1 residue, 1 model selected  

> swapaa /A: 2068 ala

Using Dunbrack library  
Swapping /A VAL 2068 to ALA  

> color sel gray

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> ui tool show Clashes

> clashes sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068A_clashes
> restrict both intraRes true ignoreHiddenModels true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    5 clashes
         atom1            atom2       overlap  distance
    /A LYS 2074 NZ   /A GLU 2064 CD    1.106    2.414
    /A PRO 2185 CB   /A ILE 2045 CD1   1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A VAL 2051 CG2  /A GLU 2044 OE1   0.606    2.694
    

  
5 clashes  

> ui tool show Contacts

> contacts sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068A_contacts
> restrict both intraRes true ignoreHiddenModels true select true color
> #00ff00 dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    238 contacts
         atom1            atom2       overlap  distance
    /A GLU 2064 CD   /A LYS 2074 NZ    1.106    2.414
    /A ILE 2045 CD1  /A PRO 2185 CB    1.100    2.660
    /A ARG 2056 NH1  /A GLU 2021 CD    0.731    2.789
    /A GLU 2064 OE1  /A LYS 2074 NZ    0.679    1.981
    /A GLU 2044 OE1  /A VAL 2051 CG2   0.606    2.694
    /A ARG 2056 CZ   /A GLU 2021 CD    0.496    2.994
    /A GLU 2021 OE2  /A ARG 2056 CZ    0.469    2.561
    /A GLU 2021 OE1  /A ARG 2056 NH1   0.445    2.215
    /A ILE 2045 CD1  /A PRO 2083 CB    0.444    3.316
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ILE 2088 CD1  /A ILE 2086 CG2   0.428    3.332
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A LYS 2065 CE   /A GLU 2075 CD    0.413    3.347
    /A GLU 2044 CD   /A VAL 2051 CG2   0.381    3.379
    /A ILE 2086 CD1  /A ILE 2084 CD1   0.375    3.385
    /A PRO 2185 CG   /A ILE 2045 CD1   0.363    3.397
    /A ILE 2084 CD1  /A ILE 2086 CG1   0.332    3.428
    /A LEU 2040 CD2  /A ILE 2025 CD1   0.291    3.469
    /A PRO 2182 CG   /A ASN 2080 OD1   0.278    3.022
    /A LYS 2074 CD   /A GLU 2064 CG    0.257    3.503
    /A GLU 2064 CD   /A LYS 2074 CE    0.254    3.506
    /A ILE 2084 CG2  /A ALA 2082 O     0.252    3.048
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ILE 2088 CG1  /A ILE 2086 CG2   0.228    3.532
    /A GLU 2064 CD   /A LYS 2074 CD    0.227    3.533
    /A LYS 2065 CE   /A GLU 2075 OE2   0.207    3.093
    /A VAL 2186 CG2  /A VAL 2188 CG2   0.205    3.555
    /A GLU 2064 OE1  /A LYS 2074 CE    0.183    3.117
    /A THR 2085 CB   /A THR 2043 OG1   0.178    3.162
    /A LYS 2065 NZ   /A GLU 2075 CD    0.174    3.346
    /A LYS 2180 O    /A GLU 2078 CA    0.158    3.142
    /A PRO 2182 CD   /A ILE 2079 O     0.140    3.160
    /A ILE 2079 CD1  /A PHE 2077 CE1   0.135    3.505
    /A ARG 2026 NH2  /A GLU 2028 OE1   0.134    2.526
    /A ILE 2084 CD1  /A LEU 2040 CD1   0.128    3.632
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A HIS 2076 CD2  /A PHE 2061 CD1   0.105    3.415
    /A HIS 2076 O    /A CYS 2062 CA    0.102    3.198
    /A GLU 2075 OE2  /A ARG 2063 CD    0.098    3.202
    /A GLU 2021 OE1  /A ARG 2056 CZ    0.084    2.946
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A LEU 2040 O    /A ARG 2026 CA    0.078    3.222
    /A ILE 2045 CG1  /A PRO 2083 CB    0.078    3.682
    /A ARG 2056 NE   /A GLU 2021 CD    0.067    3.453
    /A LYS 2074 NZ   /A GLU 2064 CG    0.056    3.464
    /A PHE 2092 CE1  /A MET 2096 CG    0.050    3.590
    /A GLU 2021 CD   /A ARG 2056 CD    0.039    3.721
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A PRO 2083 CG   /A ILE 2045 CD1   0.030    3.730
    /A GLU 2078 CD   /A ASN 2080 ND2   0.026    3.494
    /A ARG 2056 NH2  /A GLU 2021 CD    0.025    3.495
    /A GLU 2028 OE1  /A ARG 2026 CZ    0.021    3.009
    /A ILE 2071 O    /A PRO 2067 CA    0.021    3.279
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A THR 2085 OG1  /A THR 2043 CB    0.018    3.322
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A THR 2089 O    /A ILE 2088 CG2   0.013    3.287
    /A ARG 2187 O    /A THR 2085 CA    0.007    3.293
    /A VAL 2073 O    /A GLU 2064 CA    -0.003    3.303
    /A PRO 2185 O    /A PRO 2083 CA    -0.004    3.304
    /A PRO 2182 O    /A VAL 2184 CG2   -0.008    3.308
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A LEU 2040 CB   /A MET 2027 CB    -0.012    3.772
    /A ILE 2086 CG1  /A LEU 2040 CD1   -0.013    3.773
    /A THR 2043 CG2  /A THR 2085 OG1   -0.015    3.355
    /A GLU 2064 OE2  /A LYS 2074 NZ    -0.017    2.677
    /A PHE 2092 CB   /A THR 2089 OG1   -0.020    3.360
    /A GLU 2078 O    /A ILE 2060 CA    -0.021    3.321
    /A THR 2043 OG1  /A THR 2085 OG1   -0.022    2.542
    /A GLU 2078 CB   /A HIS 2076 NE2   -0.026    3.546
    /A VAL 2188 CA   /A ILE 2086 O     -0.029    3.329
    /A PHE 2077 CD2  /A CYS 2062 CB    -0.035    3.675
    /A MET 2096 CG   /A PHE 2092 CZ    -0.035    3.675
    /A GLU 2075 N    /A ARG 2063 O     -0.038    2.698
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 OE2  /A ARG 2056 NH2   -0.046    2.706
    /A ILE 2084 CG1  /A ILE 2086 CG1   -0.047    3.807
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A LYS 2074 CD   /A CYS 2062 SG    -0.062    3.712
    /A GLU 2075 OE1  /A LYS 2065 CE    -0.063    3.363
    /A VAL 2186 CA   /A ILE 2084 O     -0.066    3.366
    /A LEU 2041 CG   /A LEU 2040 O     -0.082    3.382
    /A THR 2085 O    /A LEU 2040 CA    -0.082    3.382
    /A GLU 2078 N    /A PHE 2061 O     -0.084    2.744
    /A LEU 2040 CD2  /A ILE 2025 CG1   -0.085    3.845
    /A PRO 2083 CB   /A THR 2043 O     -0.088    3.388
    /A LEU 2097 CB   /A TYR 2093 O     -0.088    3.388
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ARG 2063 N    /A HIS 2076 O     -0.094    2.754
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A CYS 2100 CB   /A PHE 2101 CD2   -0.097    3.737
    /A ILE 2079 CG1  /A PHE 2077 CE1   -0.099    3.739
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A MET 2096 CG   /A PHE 2092 O     -0.113    3.413
    /A PHE 2077 CA   /A PHE 2061 O     -0.119    3.419
    /A PRO 2185 CA   /A ILE 2045 CD1   -0.122    3.882
    /A PHE 2077 CE2  /A ILE 2060 CG2   -0.123    3.763
    /A LYS 2055 CG   /A ASP 2052 CB    -0.124    3.884
    /A ILE 2086 N    /A ARG 2187 O     -0.127    2.787
    /A VAL 2186 CG1  /A ILE 2084 CG1   -0.127    3.887
    /A PRO 2102 CA   /A LYS 2098 O     -0.129    3.429
    /A GLU 2064 OE1  /A LYS 2074 CD    -0.133    3.433
    /A PRO 2067 CB   /A ILE 2071 O     -0.134    3.434
    /A PHE 2061 CE1  /A HIS 2076 CD2   -0.135    3.655
    /A GLN 2046 CG   /A ILE 2045 O     -0.144    3.444
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A HIS 2054 N    /A ASP 2052 O     -0.150    2.810
    /A MET 2096 CB   /A PHE 2092 O     -0.151    3.451
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A LYS 2180 N    /A PHE 2077 O     -0.157    2.817
    /A ILE 2084 CG2  /A PRO 2083 O     -0.157    3.457
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A PRO 2102 CD   /A CYS 2100 C     -0.161    3.651
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ASN 2080 ND2  /A GLU 2078 CG    -0.172    3.692
    /A SER 2094 N    /A TYR 2093 CD1   -0.174    3.574
    /A PHE 2061 N    /A GLU 2078 O     -0.178    2.838
    /A ARG 2056 CA   /A LEU 2022 O     -0.178    3.478
    /A GLU 2044 O    /A THR 2043 CG2   -0.184    3.484
    /A PHE 2099 CD1  /A PHE 2099 O     -0.185    3.365
    /A ARG 2187 CB   /A THR 2085 OG1   -0.187    3.527
    /A MET 2096 O    /A PHE 2099 CB    -0.189    3.489
    /A GLU 2064 CG   /A CYS 2062 SG    -0.190    3.840
    /A GLU 2075 CA   /A ARG 2063 O     -0.194    3.494
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A PRO 2185 CD   /A VAL 2184 CG1   -0.201    3.961
    /A VAL 2186 CG1  /A PRO 2185 O     -0.201    3.501
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A GLU 2075 CB   /A ARG 2063 O     -0.208    3.508
    /A GLU 2028 CD   /A ARG 2026 NH2   -0.208    3.728
    /A ILE 2181 CG2  /A ILE 2079 O     -0.210    3.510
    /A GLU 2021 OE2  /A ARG 2056 NH1   -0.211    2.871
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A LYS 2065 NZ   /A GLU 2075 OE1   -0.212    2.872
    /A VAL 2081 CB   /A VAL 2184 CG2   -0.212    3.972
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A VAL 2051 CG2  /A GLU 2044 CG    -0.214    3.974
    /A PRO 2182 CD   /A ASN 2080 OD1   -0.215    3.515
    /A LYS 2065 N    /A VAL 2073 O     -0.215    2.875
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A VAL 2186 CG1  /A VAL 2184 CG1   -0.219    3.979
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A LYS 2055 CE   /A ASP 2052 CB    -0.234    3.994
    /A ILE 2084 CB   /A LEU 2041 O     -0.237    3.537
    /A PHE 2077 CZ   /A ILE 2079 CD1   -0.241    3.881
    /A MET 2027 N    /A LEU 2040 O     -0.242    2.902
    /A CYS 2100 N    /A PHE 2099 CD1   -0.243    3.643
    /A ILE 2181 CG1  /A LYS 2180 O     -0.245    3.545
    /A CYS 2062 SG   /A PHE 2077 CD2   -0.245    3.775
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A PHE 2101 CD2  /A CYS 2100 C     -0.249    3.619
    /A ILE 2086 CD1  /A ILE 2084 CG1   -0.249    4.009
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CG2  /A VAL 2081 CG1   -0.257    4.017
    /A LYS 2090 O    /A TYR 2093 CB    -0.258    3.558
    /A LYS 2098 CB   /A SER 2094 O     -0.260    3.560
    /A PHE 2101 CE2  /A CYS 2100 CB    -0.261    3.901
    /A THR 2089 O    /A TYR 2093 CB    -0.263    3.563
    /A GLU 2075 CD   /A ARG 2063 CD    -0.263    4.023
    /A VAL 2188 CG2  /A VAL 2186 CB    -0.264    4.024
    /A TYR 2093 CB   /A ILE 2088 CG2   -0.269    4.029
    /A PHE 2101 CB   /A LEU 2097 O     -0.271    3.571
    /A PRO 2182 O    /A ILE 2181 O     -0.272    3.112
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A LYS 2055 CD   /A ASP 2052 CB    -0.274    4.034
    /A GLU 2078 CG   /A LYS 2180 O     -0.275    3.575
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A PHE 2092 CZ   /A MET 2027 SD    -0.281    3.811
    /A VAL 2184 CG2  /A VAL 2081 O     -0.282    3.582
    /A LEU 2097 N    /A TYR 2093 O     -0.284    2.944
    /A ARG 2056 CD   /A GLU 2021 CB    -0.284    4.044
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A MET 2096 N    /A PHE 2092 O     -0.286    2.946
    /A PHE 2099 CB   /A THR 2095 O     -0.288    3.588
    /A ARG 2187 N    /A ILE 2084 O     -0.297    2.957
    /A GLU 2078 OE1  /A ASN 2080 ND2   -0.298    2.958
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A ASP 2052 OD2  /A LYS 2055 CE    -0.303    3.603
    /A VAL 2184 CG1  /A VAL 2081 O     -0.309    3.609
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A THR 2053 N    /A VAL 2051 O     -0.312    2.972
    /A PHE 2101 N    /A LEU 2097 O     -0.315    2.975
    /A ARG 2056 CB   /A LEU 2022 O     -0.318    3.618
    /A PRO 2185 O    /A VAL 2184 CG1   -0.324    3.624
    /A LYS 2074 CA   /A ARG 2063 O     -0.325    3.625
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A LYS 2074 CE   /A GLU 2064 CG    -0.333    4.093
    /A PRO 2102 N    /A LYS 2098 O     -0.335    3.395
    /A GLU 2183 O    /A VAL 2184 CG2   -0.335    3.635
    /A PRO 2083 O    /A THR 2043 N     -0.338    2.998
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A PHE 2099 N    /A THR 2095 O     -0.344    3.004
    /A ILE 2181 CA   /A ILE 2079 O     -0.346    3.646
    /A PRO 2050 CD   /A MET 2049 CG    -0.347    4.107
    /A LEU 2041 CD2  /A LEU 2040 O     -0.348    3.648
    /A ASP 2048 OD1  /A LYS 2047 C     -0.349    3.379
    /A THR 2095 CB   /A LYS 2091 O     -0.352    3.652
    /A ALA 2087 O    /A ILE 2088 CG1   -0.357    3.657
    /A SER 2094 OG   /A LYS 2091 CA    -0.359    3.699
    /A GLU 2021 OE2  /A ARG 2056 NE    -0.359    3.019
    /A PHE 2101 CA   /A LEU 2097 O     -0.360    3.660
    /A THR 2085 CA   /A THR 2043 OG1   -0.361    3.701
    /A PRO 2185 CB   /A ILE 2045 CG1   -0.366    4.126
    /A ASN 2080 OD1  /A GLU 2078 OE1   -0.371    3.211
    /A PRO 2067 N    /A LYS 2065 O     -0.372    3.432
    /A ALA 2066 O    /A LYS 2065 O     -0.372    3.212
    /A TYR 2093 N    /A THR 2089 O     -0.372    3.032
    /A PHE 2077 CZ   /A ILE 2079 CG1   -0.374    4.014
    /A LYS 2091 O    /A SER 2094 OG    -0.377    2.857
    /A ILE 2181 CG1  /A ILE 2079 CB    -0.377    4.137
    /A THR 2095 O    /A LYS 2098 CB    -0.380    3.680
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A LYS 2065 CD   /A GLU 2075 CD    -0.381    4.141
    /A ARG 2187 CB   /A THR 2085 CA    -0.383    4.143
    /A ILE 2079 N    /A LYS 2180 O     -0.384    3.044
    /A LYS 2055 N    /A ASP 2052 O     -0.384    3.044
    /A PRO 2185 O    /A PRO 2083 CB    -0.386    3.686
    /A PHE 2099 CA   /A MET 2096 O     -0.386    3.686
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ILE 2071 CB   /A ALA 2068 O     -0.390    3.690
    /A ARG 2056 CD   /A GLU 2021 CG    -0.391    4.151
    /A THR 2043 CB   /A THR 2085 N     -0.393    3.913
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A PHE 2092 CD1  /A MET 2096 CG    -0.394    4.034
    /A THR 2089 CA   /A ILE 2088 CG2   -0.395    4.155
    /A GLU 2078 CA   /A PHE 2061 O     -0.397    3.697
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    /A ILE 2181 CD1  /A ILE 2079 CD1   -0.400    4.160
    

  
238 contacts  

> select /A:2270-2300

247 atoms, 249 bonds, 31 residues, 1 model selected  

> select /A:2270-2300

247 atoms, 249 bonds, 31 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 243 pseudobonds, 81 residues, 3 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/OrangeOnly/orange_V2068A_hbonds
> color #aa00ff dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A ALA 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A ALA 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

——— End of log from Fri May 2 10:11:43 2025 ———

> view name session-start

opened ChimeraX session  

> close #1.1-3

> select /A:2198

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2198-2239

348 atoms, 356 bonds, 42 residues, 1 model selected  

> select /A:2198-2199

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:2198-2238

343 atoms, 351 bonds, 41 residues, 1 model selected  

> color sel purple

> select add #1

18467 atoms, 18841 bonds, 2300 residues, 1 model selected  

> hide sel atoms

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2058,2081

15 atoms, 13 bonds, 2 residues, 1 model selected  

> show sel atoms

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

> select /A:1977

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

> select /A:1977-2003

212 atoms, 214 bonds, 27 residues, 1 model selected  

> color sel cornflower blue

> select /A:1976

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1741-1976

1886 atoms, 1914 bonds, 236 residues, 1 model selected  

> hide sel cartoons

> select /A:1740

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:1291-1740

3589 atoms, 3663 bonds, 450 residues, 1 model selected  

> hide sel cartoons

> select /A:1290

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

> select /A:963-1290

2634 atoms, 2702 bonds, 328 residues, 1 model selected  

> hide sel cartoons

> select /A:962

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:541-962

3403 atoms, 3476 bonds, 422 residues, 1 model selected  

> hide sel cartoons

> select /A:540

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:1-540

4362 atoms, 4446 bonds, 540 residues, 1 model selected  

> hide sel cartoons

[Repeated 1 time(s)]

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2004

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

> select /A:2004-2018

125 atoms, 127 bonds, 15 residues, 1 model selected  

> select /A:2239

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:2239-2300

490 atoms, 496 bonds, 62 residues, 1 model selected  

> hide sel cartoons

> select /A:2056

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

> select /A:2056-2102

377 atoms, 386 bonds, 47 residues, 1 model selected  

> color sel orange

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> save
> C:/Users/emirm/Desktop/Fly/Chimera_WorkingFolder/Contacts_Modeling_Chimera/Human_Fly_Superposition_Foldseek_StructuralAnalysis.cxs

——— End of log from Fri Jul 25 15:41:25 2025 ———

> view name session-start

opened ChimeraX session  

> ui windowfill toggle

> select clear

> ui mousemode right select

Drag select of 269 residues  

> cartoon style sel xsection oval modeHelix default

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> cartoon style sel xsection oval modeHelix default

> ui windowfill toggle

> select clear

> select /A:2208

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2208-2209

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> select /A:2208-2209

15 atoms, 15 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2229-2230

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select /A:2229-2233

41 atoms, 40 bonds, 5 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    48 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N    /A ILE 2060 O    no hydrogen  2.857  N/A
    /A LEU 2022 N    /A LEU 2058 O    no hydrogen  2.913  N/A
    /A MET 2027 N    /A LEU 2040 O    no hydrogen  2.902  N/A
    /A LEU 2040 N    /A MET 2027 O    no hydrogen  3.331  N/A
    /A LEU 2041 N    /A THR 2085 O    no hydrogen  3.063  N/A
    /A THR 2043 N    /A PRO 2083 O    no hydrogen  2.998  N/A
    /A THR 2043 OG1  /A LEU 2041 O    no hydrogen  3.223  N/A
    /A THR 2043 OG1  /A THR 2085 OG1  no hydrogen  2.542  N/A
    /A LYS 2055 N    /A ASP 2052 O    no hydrogen  3.044  N/A
    /A VAL 2057 N    /A LEU 2022 O    no hydrogen  2.815  N/A
    /A LEU 2058 N    /A LEU 2022 O    no hydrogen  3.346  N/A
    /A ARG 2059 N    /A ASN 2080 O    no hydrogen  2.872  N/A
    /A ILE 2060 N    /A LEU 2020 O    no hydrogen  2.817  N/A
    /A PHE 2061 N    /A GLU 2078 O    no hydrogen  2.838  N/A
    /A CYS 2062 SG   /A HIS 2076 O    no hydrogen  3.931  N/A
    /A ARG 2063 N    /A HIS 2076 O    no hydrogen  2.754  N/A
    /A LYS 2065 N    /A VAL 2073 O    no hydrogen  2.875  N/A
    /A LYS 2065 NZ   /A GLU 2075 OE1  no hydrogen  2.872  N/A
    /A ALA 2068 N    /A ILE 2071 O    no hydrogen  3.122  N/A
    /A ILE 2071 N    /A ALA 2068 O    no hydrogen  3.161  N/A
    /A LYS 2074 NZ   /A GLU 2064 OE1  no hydrogen  1.981  N/A
    /A GLU 2075 N    /A ARG 2063 O    no hydrogen  2.698  N/A
    /A HIS 2076 N    /A ARG 2063 O    no hydrogen  3.251  N/A
    /A HIS 2076 NE2  /A GLU 2078 OE2  no hydrogen  3.168  N/A
    /A GLU 2078 N    /A PHE 2061 O    no hydrogen  2.744  N/A
    /A ILE 2079 N    /A LYS 2180 O    no hydrogen  3.044  N/A
    /A ASN 2080 N    /A ARG 2059 O    no hydrogen  2.752  N/A
    /A ASN 2080 ND2  /A GLU 2078 OE1  no hydrogen  2.958  N/A
    /A ALA 2082 N    /A VAL 2057 O    no hydrogen  2.859  N/A
    /A THR 2085 N    /A LEU 2041 O    no hydrogen  2.749  N/A
    /A THR 2085 OG1  /A THR 2043 OG1  no hydrogen  2.542  N/A
    /A ILE 2086 N    /A ARG 2187 O    no hydrogen  2.787  N/A
    /A PHE 2092 N    /A THR 2089 OG1  no hydrogen  3.214  N/A
    /A TYR 2093 N    /A THR 2089 O    no hydrogen  3.032  N/A
    /A SER 2094 N    /A LYS 2090 O    no hydrogen  3.087  N/A
    /A SER 2094 OG   /A LYS 2090 O    no hydrogen  3.475  N/A
    /A SER 2094 OG   /A LYS 2091 O    no hydrogen  2.857  N/A
    /A THR 2095 N    /A LYS 2091 O    no hydrogen  3.066  N/A
    /A THR 2095 OG1  /A LYS 2091 O    no hydrogen  3.063  N/A
    /A MET 2096 N    /A PHE 2092 O    no hydrogen  2.946  N/A
    /A LEU 2097 N    /A TYR 2093 O    no hydrogen  2.944  N/A
    /A LYS 2098 N    /A SER 2094 O    no hydrogen  3.125  N/A
    /A PHE 2099 N    /A THR 2095 O    no hydrogen  3.004  N/A
    /A CYS 2100 N    /A MET 2096 O    no hydrogen  3.088  N/A
    /A CYS 2100 SG   /A MET 2096 O    no hydrogen  3.546  N/A
    /A PHE 2101 N    /A LEU 2097 O    no hydrogen  2.975  N/A
    /A LYS 2180 N    /A PHE 2077 O    no hydrogen  2.817  N/A
    /A ARG 2187 N    /A ILE 2084 O    no hydrogen  2.957  N/A
    

  
48 hydrogen bonds found  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> select /A:2244

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2244-2245

18 atoms, 18 bonds, 2 residues, 1 model selected  

> select /A:2020-2028,2040-2102,2180-2188

649 atoms, 660 bonds, 81 residues, 1 model selected  

> select /A:2180

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

> select /A:2180-2188

72 atoms, 73 bonds, 9 residues, 1 model selected  

> select /A:2020

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2028

73 atoms, 72 bonds, 9 residues, 1 model selected  

> select /A:1977-1978

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select /A:1977-1980

34 atoms, 34 bonds, 4 residues, 1 model selected  

> select /A:1977

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

> select /A:1977-1994

153 atoms, 155 bonds, 18 residues, 1 model selected  

> select /A:1977

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

> select /A:1977-2003

212 atoms, 214 bonds, 27 residues, 1 model selected  

> ui windowfill toggle

> select /A:2059

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

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel cyan

> color sel black

> color sel lime

> select clear

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color sel red

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOut.tif width 1280 height 491
> supersample 3

Drag select of 67 atoms, 262 residues, 54 bonds  

> show sel surfaces

> transparency (#!1 & sel) 70

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOutSurface.tif width 1280 height
> 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
303175 of 2695328 triangles, 67 atoms, 262 residues, 54 bonds  

> hide sel surfaces

> ui windowfill toggle

> select clear

> ui windowfill toggle

> select clear

[Repeated 1 time(s)]

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) orange

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add /A:2056

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add /A:2058

26 atoms, 23 bonds, 3 residues, 2 models selected  

> select add /A:2059

37 atoms, 33 bonds, 4 residues, 2 models selected  

> select add /A:2060

45 atoms, 40 bonds, 5 residues, 2 models selected  

> select add /A:2079

53 atoms, 47 bonds, 6 residues, 2 models selected  

> select add /A:2080

61 atoms, 54 bonds, 7 residues, 2 models selected  

> select add /A:2081

68 atoms, 60 bonds, 8 residues, 2 models selected  
Drag select of 67 atoms, 262 residues, 54 bonds  

> hide sel atoms

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) orange

> color (#!1 & sel) red

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOut.tif width 1280 height 491
> supersample 3

Drag select of 262 residues  

> show sel surfaces

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOutSurface.tif width 1280 height
> 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
301155 of 2695328 triangles, 262 residues  

> hide sel surfaces

> select clear

> select /A:2081

7 atoms, 6 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) orange red

> color (#!1 & sel) orange

> select clear

> select /A:2056

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

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add /A:2056

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select add /A:2058

26 atoms, 23 bonds, 3 residues, 2 models selected  

> select add /A:2059

37 atoms, 33 bonds, 4 residues, 2 models selected  

> select add /A:2060

45 atoms, 40 bonds, 5 residues, 2 models selected  

> select add /A:2079

53 atoms, 47 bonds, 6 residues, 2 models selected  

> select add /A:2080

61 atoms, 54 bonds, 7 residues, 2 models selected  

> select add /A:2081

68 atoms, 60 bonds, 8 residues, 2 models selected  

> select add /A:2082

73 atoms, 64 bonds, 9 residues, 2 models selected  

> select add /A:2083

80 atoms, 71 bonds, 10 residues, 2 models selected  

> select add /A:2020

88 atoms, 78 bonds, 11 residues, 2 models selected  

> select add /A:2021

97 atoms, 86 bonds, 12 residues, 2 models selected  

> select add /A:2022

105 atoms, 93 bonds, 13 residues, 2 models selected  

> select add /A:2023

109 atoms, 96 bonds, 14 residues, 2 models selected  

> select add /A:2042

114 atoms, 100 bonds, 15 residues, 2 models selected  

> select add /A:2041

122 atoms, 107 bonds, 16 residues, 2 models selected  

> select add /A:2084

130 atoms, 114 bonds, 17 residues, 2 models selected  

> select add /A:2085

137 atoms, 120 bonds, 18 residues, 2 models selected  

> select add /A:2024

145 atoms, 127 bonds, 19 residues, 2 models selected  

> select add /A:2025

153 atoms, 134 bonds, 20 residues, 2 models selected  

> select add /A:2026

164 atoms, 144 bonds, 21 residues, 2 models selected  

> ui windowfill toggle

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    1 clashes
         atom1           atom2       overlap  distance
    /A ARG 2056 NH1  /A GLU 2021 CD   0.731    2.789
    

  
1 clashes  

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> select add #1.2

164 atoms, 161 bonds, 1 pseudobond, 21 residues, 3 models selected  

> select subtract #1.2

164 atoms, 161 bonds, 21 residues, 2 models selected  

> show #1.1 models

> select subtract #1.1

1 model selected  

> select add #1.1

18467 atoms, 2300 residues, 1 model selected  

> select subtract #1.1

1 model selected  

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> close #1.1-2

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select subtract /A:2021

155 atoms, 151 bonds, 20 residues, 1 model selected  

> select subtract /A:2022

147 atoms, 143 bonds, 19 residues, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select clear

> select /A:2058

8 atoms, 7 bonds, 1 residue, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2057-2058

15 atoms, 14 bonds, 2 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    0 contacts
    atom1  atom2  overlap  distance
    

  
No contacts  

> select /A:2057

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2057-2058

15 atoms, 14 bonds, 2 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    0 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    

  
0 hydrogen bonds found  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 21 residues, 1 model selected  

> select subtract /A:2056

153 atoms, 150 bonds, 20 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    51 contacts
         atom1            atom2       overlap  distance
    /A GLY 2023 O    /A VAL 2057 CG2   0.429    2.871
    /A ARG 2026 CG   /A LEU 2041 CD2   0.424    3.336
    /A ALA 2082 O    /A ILE 2084 CG2   0.252    3.048
    /A VAL 2057 CG1  /A ILE 2025 CG2   0.239    3.521
    /A ARG 2026 CD   /A LEU 2041 CD2   0.105    3.655
    /A VAL 2081 CG2  /A LEU 2058 CD1   0.082    3.678
    /A ARG 2059 CA   /A LEU 2020 O     0.034    3.266
    /A LEU 2058 CD1  /A ARG 2059 N     0.020    3.500
    /A ILE 2084 CA   /A LEU 2041 O     0.016    3.284
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.009    3.769
    /A ILE 2025 CB   /A LEU 2022 CD2   -0.043    3.803
    /A VAL 2081 CG2  /A ILE 2079 CG2   -0.044    3.804
    /A GLU 2021 N    /A LEU 2020 CD2   -0.059    3.579
    /A ALA 2082 CB   /A VAL 2057 CA    -0.060    3.820
    /A THR 2085 N    /A LEU 2041 O     -0.089    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.092    2.752
    /A ALA 2082 O    /A VAL 2081 CG1   -0.094    3.394
    /A LEU 2058 CD1  /A ASN 2080 O     -0.101    3.401
    /A ILE 2079 CG2  /A LEU 2058 CD1   -0.148    3.908
    /A VAL 2057 N    /A LEU 2022 O     -0.155    2.815
    /A VAL 2081 CA   /A VAL 2057 O     -0.156    3.456
    /A PRO 2083 O    /A ILE 2084 CG2   -0.157    3.457
    /A ILE 2060 N    /A LEU 2020 O     -0.157    2.817
    /A LEU 2058 O    /A GLU 2021 CA    -0.162    3.462
    /A ASN 2080 O    /A LEU 2058 CA    -0.164    3.464
    /A ILE 2060 O    /A LEU 2020 N     -0.197    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.199    2.859
    /A ALA 2042 CB   /A VAL 2057 CG2   -0.199    3.959
    /A LEU 2041 CD2  /A ARG 2026 CB    -0.205    3.965
    /A ARG 2059 N    /A ASN 2080 O     -0.212    2.872
    /A GLU 2021 CG   /A LEU 2020 O     -0.213    3.513
    /A LEU 2058 CD2  /A ILE 2060 CD1   -0.214    3.974
    /A ILE 2025 N    /A ASN 2024 OD1   -0.218    2.878
    /A LEU 2020 CD2  /A LEU 2020 O     -0.220    3.520
    /A ILE 2084 CB   /A LEU 2041 O     -0.237    3.537
    /A VAL 2057 CB   /A GLY 2023 O     -0.249    3.549
    /A LEU 2022 N    /A LEU 2058 O     -0.253    2.913
    /A ILE 2084 CG2  /A VAL 2081 CG1   -0.257    4.017
    /A ILE 2079 CA   /A ARG 2059 O     -0.274    3.574
    /A ASN 2024 O    /A LEU 2022 CG    -0.276    3.576
    /A VAL 2057 CG2  /A GLY 2023 C     -0.285    3.775
    /A ASN 2080 CA   /A ARG 2059 O     -0.303    3.603
    /A LEU 2058 CB   /A LEU 2022 CB    -0.311    4.071
    /A LEU 2058 CG   /A ILE 2060 CG1   -0.329    4.089
    /A ILE 2060 CG1  /A LEU 2058 CD1   -0.330    4.090
    /A VAL 2057 O    /A ALA 2082 CB    -0.342    3.642
    /A VAL 2081 CG2  /A ASN 2080 O     -0.380    3.680
    /A ARG 2059 CB   /A ASN 2080 CB    -0.387    4.147
    /A ARG 2026 NE   /A LEU 2041 CD2   -0.393    3.913
    /A ILE 2025 CD1  /A LEU 2022 CD2   -0.397    4.157
    /A ASN 2080 CB   /A ARG 2059 O     -0.399    3.699
    

  
51 contacts  

> hide sel cartoons

> select clear

> ui windowfill toggle

> select clear

> ui mousemode right translate

> ui windowfill toggle

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select subtract /A:2056

153 atoms, 150 bonds, 51 pseudobonds, 20 residues, 2 models selected  

> style sel ball

Changed 153 atom styles  

> style sel stick

Changed 153 atom styles  

> ui windowfill toggle

> select clear

> save C:/Users/emirm/Desktop/contacts/l2058_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

164 atoms, 161 bonds, 51 pseudobonds, 21 residues, 2 models selected  

> select subtract /A:2056

153 atoms, 150 bonds, 51 pseudobonds, 20 residues, 2 models selected  

> hide #1.3 models

> hide #1.2 models

> show #1.3 models

> hide #1.3 models

> close #1.3

> hide #1.1 models

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    10 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N  /A ILE 2060 O  no hydrogen  2.857  N/A
    /A LEU 2022 N  /A LEU 2058 O  no hydrogen  2.913  N/A
    /A LEU 2041 N  /A THR 2085 O  no hydrogen  3.063  N/A
    /A VAL 2057 N  /A LEU 2022 O  no hydrogen  2.815  N/A
    /A LEU 2058 N  /A LEU 2022 O  no hydrogen  3.346  N/A
    /A ARG 2059 N  /A ASN 2080 O  no hydrogen  2.872  N/A
    /A ILE 2060 N  /A LEU 2020 O  no hydrogen  2.817  N/A
    /A ASN 2080 N  /A ARG 2059 O  no hydrogen  2.752  N/A
    /A ALA 2082 N  /A VAL 2057 O  no hydrogen  2.859  N/A
    /A THR 2085 N  /A LEU 2041 O  no hydrogen  2.749  N/A
    

  
10 hydrogen bonds found  

> ui windowfill toggle

> select clear

> save C:/Users/emirm/Desktop/contacts/l2058_hb.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.3 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> swapaa /A: 2058 pro

Using Dunbrack library  
/A LEU 2058: phi -137.9, psi 132.6 trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /A PRO 2058  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

163 atoms, 161 bonds, 53 pseudobonds, 21 residues, 3 models selected  

> select subtract /A:2056

152 atoms, 150 bonds, 53 pseudobonds, 20 residues, 3 models selected  

> ui windowfill toggle

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    1 clashes
        atom1            atom2       overlap  distance
    /A PRO 2058 CD  /A VAL 2057 CG1   0.963    2.797
    

  
1 clashes  

> ui windowfill toggle

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select subtract #1.2

152 atoms, 150 bonds, 10 pseudobonds, 20 residues, 2 models selected  

> select subtract #1.3

152 atoms, 150 bonds, 20 residues, 1 model selected  

> close #1.2-3

> ui windowfill toggle

> ui tool show Clashes

> color bfactor sel

152 atoms, 20 residues, atom bfactor range 49.1 to 89.1  

> undo

> ui tool show Clashes

> ui windowfill toggle

> close #1.1

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

152 atoms, 150 bonds, 20 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2056-2060,2079-2085

163 atoms, 161 bonds, 21 residues, 1 model selected  

> select /A:2057-2058

14 atoms, 14 bonds, 2 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

152 atoms, 150 bonds, 20 residues, 1 model selected  

> ui tool show "Add Hydrogens"

> addh

Summary of feedback from adding hydrogens to
fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
notes | Termini for fold_2025_02_26_14_57_hob_native_model_0.cif (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 2300  
Chain-final residues that are not actual C termini:  
1901 hydrogen bonds  
18569 hydrogens added  
  

> ui windowfill toggle

> ui tool show "Color Actions"

> ui windowfill toggle

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    1 clashes
        atom1            atom2       overlap  distance
    /A PRO 2058 CD  /A VAL 2057 CG1   0.603    2.797
    

  
1 clashes  

> ui windowfill toggle

[Repeated 1 time(s)]

> color bfactor sel

152 atoms, 20 residues, atom bfactor range 49.1 to 89.1  

> undo

> style sel ball

Changed 152 atom styles  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    30 contacts
         atom1            atom2       overlap  distance
    /A VAL 2057 CG1  /A PRO 2058 CD    0.603    2.797
    /A VAL 2057 CG2  /A GLY 2023 O     0.249    2.871
    /A ILE 2084 CG2  /A ALA 2082 O     0.072    3.048
    /A LEU 2041 CD2  /A ARG 2026 CG    0.064    3.336
    /A THR 2085 N    /A LEU 2041 O     -0.104    2.749
    /A ASN 2080 N    /A ARG 2059 O     -0.107    2.752
    /A PRO 2058 CG   /A VAL 2057 CG1   -0.112    3.512
    /A VAL 2057 CG1  /A ILE 2025 CG2   -0.121    3.521
    /A ARG 2059 CA   /A LEU 2020 O     -0.146    3.266
    /A ILE 2084 CA   /A LEU 2041 O     -0.164    3.284
    /A VAL 2057 N    /A LEU 2022 O     -0.170    2.815
    /A ILE 2060 N    /A LEU 2020 O     -0.172    2.817
    /A ILE 2060 O    /A LEU 2020 N     -0.212    2.857
    /A ALA 2082 N    /A VAL 2057 O     -0.214    2.859
    /A ARG 2059 N    /A ASN 2080 O     -0.227    2.872
    /A ILE 2025 N    /A ASN 2024 OD1   -0.233    2.878
    /A GLU 2021 N    /A LEU 2020 CD2   -0.254    3.579
    /A ARG 2026 CD   /A LEU 2041 CD2   -0.255    3.655
    /A LEU 2022 N    /A PRO 2058 O     -0.268    2.913
    /A ALA 2082 O    /A VAL 2081 CG1   -0.274    3.394
    /A PRO 2058 CD   /A LEU 2022 O     -0.283    3.403
    /A PRO 2058 N    /A LEU 2022 O     -0.286    3.346
    /A VAL 2081 CA   /A VAL 2057 O     -0.336    3.456
    /A PRO 2083 O    /A ILE 2084 CG2   -0.337    3.457
    /A PRO 2058 O    /A GLU 2021 CA    -0.342    3.462
    /A ASN 2080 O    /A PRO 2058 CA    -0.344    3.464
    /A PRO 2058 CG   /A VAL 2057 CB    -0.369    3.769
    /A ASN 2024 CA   /A VAL 2057 CG2   -0.369    3.769
    /A LEU 2022 CB   /A PRO 2058 CD    -0.391    3.791
    /A GLU 2021 CG   /A LEU 2020 O     -0.393    3.513
    

  
30 contacts  

> ui windowfill toggle

[Repeated 1 time(s)]

> style sel stick

Changed 43 atom styles  

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2085

14 atoms, 13 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 30 pseudobonds, 20 residues, 2 models selected  

> select /A:2079-2085

106 atoms, 106 bonds, 3 pseudobonds, 7 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 30 pseudobonds, 20 residues, 2 models selected  

> style sel stick

Changed 325 atom styles  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> ui windowfill toggle

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    130 contacts
         atom1             atom2        overlap  distance
    /A PRO 2058 HD2   /A VAL 2057 CB     1.082    1.618
    /A PRO 2058 HD2   /A VAL 2057 CG1    0.984    1.716
    /A VAL 2057 HB    /A PRO 2058 CD     0.618    2.082
    /A VAL 2057 CG1   /A PRO 2058 CD     0.603    2.797
    /A VAL 2057 HB    /A PRO 2058 HD2    0.482    1.518
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A PRO 2058 HD2   /A VAL 2057 HG13   0.201    1.799
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A PRO 2058 HD2   /A VAL 2057 HG12   0.194    1.806
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2022 HD21  /A PRO 2058 HG3    0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HB3   /A PRO 2058 HD3    0.025    1.975
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A VAL 2057 HB    /A PRO 2058 HD3    0.015    1.985
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A VAL 2057 HG13  /A PRO 2058 CD     -0.013    2.713
    /A VAL 2057 HG12  /A PRO 2058 CD     -0.013    2.713
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A LEU 2022 HB3   /A PRO 2058 CD     -0.097    2.797
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A PRO 2058 CG    /A VAL 2057 CG1    -0.112    3.512
    /A VAL 2057 CB    /A PRO 2058 HD3    -0.115    2.815
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2022 HD21  /A PRO 2058 CG     -0.135    2.835
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A LEU 2022 CB    /A PRO 2058 HD3    -0.144    2.844
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A PRO 2058 HD3   /A LEU 2022 O      -0.277    2.697
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A PRO 2058 CD    /A LEU 2022 O      -0.283    3.403
    /A PRO 2058 N     /A LEU 2022 O      -0.286    3.346
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 HG3   /A LEU 2022 CD2    -0.297    2.997
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A PRO 2058 HB2   /A LEU 2022 HB3    -0.354    2.354
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.357    3.057
    /A LEU 2022 HB3   /A PRO 2058 CB     -0.361    3.061
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A PRO 2058 CG    /A VAL 2057 CB     -0.369    3.769
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A LEU 2022 CB    /A PRO 2058 CD     -0.391    3.791
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A PRO 2058 HG2   /A VAL 2057 O      -0.393    2.813
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.400    3.100
    

  
130 contacts  

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true color
> #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> ui windowfill toggle

[Repeated 2 time(s)]

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> select add #1.1

146 atoms, 130 pseudobonds, 20 residues, 2 models selected  

> select subtract #1.1

146 atoms, 20 residues, 1 model selected  

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058p_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.1 models

> show #1.1 models

> show #1.2 models

> hide #1.1 models

> ui windowfill toggle

> select add /A:2022@CG

1 atom, 1 residue, 1 model selected  

> select subtract /A:2022@CG

Nothing selected  

> select add /A:2022@CA

1 atom, 1 residue, 1 model selected  

> ui windowfill toggle

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 134 pseudobonds, 20 residues, 3 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> hide sel atoms

> show sel atoms

> show sel cartoons

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> show sel atoms

> hide sel cartoons

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058p_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 134 pseudobonds, 20 residues, 3 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> hide sel atoms

> show sel atoms

[Repeated 1 time(s)]

> hide sel atoms

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> save C:/Users/emirm/Desktop/contacts/l2058p_cla2.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.2 models

> hide #!1 models

> show #!1 models

> show #1.1 models

> select add #1.1

130 pseudobonds, 1 model selected  

> select subtract #1.1

Nothing selected  

> select add #1.1

130 pseudobonds, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true

Atom specifier selects no atoms  

> select subtract #1.1

Nothing selected  

> hide #1.1 models

> show #1.1 models

> select add #1

37035 atoms, 37410 bonds, 134 pseudobonds, 2300 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 134 pseudobonds, 20 residues, 3 models selected  

> ui tool show Contacts

> close #1.1-2

> ui tool show Contacts

Restriction atom specifier must not be blank  

> ui tool show Contacts

> contacts sel intraRes true ignoreHiddenModels true select true color #ffffff
> dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    323 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 CB    /A PRO 2058 HD2    1.082    1.618
    /A VAL 2057 CG1   /A PRO 2058 HD2    0.984    1.716
    /A GLU 2021 CD    /A ARG 2056 NH1    0.716    2.789
    /A PRO 2083 HB3   /A ILE 2045 HD12   0.629    1.371
    /A PRO 2058 CD    /A VAL 2057 HB     0.618    2.082
    /A PRO 2058 CD    /A VAL 2057 CG1    0.603    2.797
    /A THR 2085 HG1   /A THR 2043 OG1    0.505    1.595
    /A GLU 2021 CD    /A ARG 2056 CZ     0.496    2.994
    /A PRO 2058 HD2   /A VAL 2057 HB     0.482    1.518
    /A GLU 2021 OE2   /A ARG 2056 CZ     0.469    2.561
    /A ALA 2082 O     /A ILE 2084 HG22   0.435    1.985
    /A GLU 2021 OE1   /A ARG 2056 NH1    0.430    2.215
    /A ASN 2080 OD1   /A PRO 2182 HG2    0.403    2.017
    /A PRO 2083 HB3   /A ILE 2045 CD1    0.352    2.348
    /A VAL 2057 HG23  /A ASN 2024 HA     0.336    1.664
    /A VAL 2057 HG12  /A ILE 2025 HG21   0.327    1.673
    /A ASN 2024 HB3   /A SER 2002 OG     0.311    2.189
    /A PRO 2083 CB    /A ILE 2045 HD12   0.299    2.401
    /A LEU 2041 CD2   /A ARG 2026 HG3    0.297    2.403
    /A THR 2085 HG1   /A THR 2043 CB     0.286    2.414
    /A ASN 2080 HD22  /A GLU 2078 CD     0.273    2.607
    /A ASN 2080 H     /A ARG 2059 O      0.258    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.249    2.871
    /A THR 2085 H     /A LEU 2041 O      0.230    1.790
    /A ARG 2026 O     /A VAL 2000 H      0.204    1.816
    /A VAL 2057 HG13  /A PRO 2058 HD2    0.201    1.799
    /A ILE 2060 H     /A LEU 2020 O      0.195    1.825
    /A VAL 2057 HG12  /A PRO 2058 HD2    0.194    1.806
    /A ILE 2025 CG2   /A VAL 2057 HG12   0.191    2.509
    /A ARG 2026 HA    /A LEU 2040 O      0.189    2.231
    /A GLU 2021 H     /A LEU 2005 O      0.173    1.847
    /A ILE 2060 O     /A LEU 2020 H      0.170    1.850
    /A ALA 2082 H     /A VAL 2057 O      0.168    1.852
    /A VAL 2057 O     /A VAL 2057 HG13   0.156    2.264
    /A ILE 2084 HG21  /A ILE 2084 HD11   0.156    1.844
    /A ASN 2080 O     /A ARG 2059 H      0.148    1.872
    /A ASN 2024 CB    /A SER 2002 OG     0.136    3.064
    /A LEU 2020 O     /A ARG 2059 HA     0.122    2.298
    /A ARG 2059 HE    /A LEU 2019 HD13   0.121    1.879
    /A ILE 2079 O     /A PRO 2182 HD3    0.120    2.300
    /A ARG 2026 NH2   /A GLU 2028 OE1    0.119    2.526
    /A ALA 2082 O     /A VAL 2081 HG11   0.113    2.307
    /A PRO 2083 HB2   /A THR 2043 O      0.108    2.312
    /A LEU 2020 C     /A LEU 2020 HD21   0.098    2.512
    /A ASN 2080 OD1   /A PRO 2182 CG     0.098    3.022
    /A LEU 2041 HD13  /A ASP 2038 CG     0.096    2.784
    /A ILE 2079 HD11  /A PHE 2077 CE1    0.091    2.609
    /A ILE 2084 O     /A ILE 2084 HG13   0.085    2.335
    /A PRO 2083 CB    /A ILE 2045 CD1    0.084    3.316
    /A GLU 2021 OE1   /A ARG 2056 CZ     0.084    2.946
    /A THR 2085 H     /A THR 2043 HG1    0.084    1.916
    /A VAL 2057 CG1   /A ILE 2025 HG21   0.083    2.617
    /A PRO 2083 HA    /A PRO 2185 O      0.076    2.344
    /A ALA 2082 O     /A ILE 2084 CG2    0.072    3.048
    /A ARG 2026 CG    /A LEU 2041 CD2    0.064    3.336
    /A THR 2085 OG1   /A THR 2043 OG1    0.058    2.542
    /A ILE 2060 HA    /A GLU 2078 O      0.053    2.367
    /A PRO 2058 HG3   /A LEU 2022 HD21   0.053    1.947
    /A GLU 2021 CD    /A ARG 2056 NE     0.052    3.453
    /A THR 2085 HA    /A ARG 2187 O      0.051    2.369
    /A ARG 2059 HD2   /A ARG 2059 HH11   0.047    1.953
    /A ILE 2084 O     /A ARG 2187 H      0.043    1.977
    /A THR 2085 HG1   /A THR 2043 CG2    0.042    2.658
    /A THR 2085 CB    /A THR 2043 OG1    0.038    3.162
    /A ILE 2084 HD12  /A ILE 2086 CG1    0.027    2.673
    /A THR 2085 O     /A LEU 2040 HA     0.026    2.394
    /A PRO 2058 HD3   /A LEU 2022 HB3    0.025    1.975
    /A PRO 2083 O     /A THR 2043 H      0.023    1.997
    /A ARG 2026 CZ    /A GLU 2028 OE1    0.021    3.009
    /A PRO 2058 O     /A LEU 2022 H      0.018    2.002
    /A ILE 2084 CD1   /A ILE 2086 CD1    0.015    3.385
    /A PRO 2058 HD3   /A VAL 2057 HB     0.015    1.985
    /A LEU 2041 HD23  /A ARG 2026 HG3    0.013    1.987
    /A ILE 2079 HD11  /A PHE 2077 HE1    0.013    1.987
    /A LEU 2041 HD22  /A ARG 2026 HG3    0.013    1.987
    /A ASN 2080 ND2   /A GLU 2078 CD     0.011    3.494
    /A THR 2085 N     /A THR 2043 HG1    0.011    2.614
    /A GLU 2021 CD    /A ARG 2056 NH2    0.010    3.495
    /A ARG 2059 HE    /A LEU 2019 CD1    0.010    2.690
    /A ILE 2084 HD12  /A LEU 2040 CD1    0.009    2.691
    /A GLU 2021 O     /A LEU 2005 H      0.008    2.012
    /A LEU 2041 CD1   /A ASP 2038 HB3    0.006    2.694
    /A LEU 2041 HD13  /A ASP 2038 CB     -0.001    2.701
    /A ASN 2080 HD22  /A GLU 2078 OE1    -0.004    2.024
    /A ASN 2080 HB3   /A ARG 2059 HB3    -0.009    2.009
    /A PRO 2058 CD    /A VAL 2057 HG13   -0.013    2.713
    /A PRO 2058 CD    /A VAL 2057 HG12   -0.013    2.713
    /A VAL 2057 CG2   /A ASN 2024 HA     -0.023    2.723
    /A ARG 2026 H     /A VAL 2000 O      -0.023    2.043
    /A LEU 2022 CD2   /A ILE 2025 HB     -0.023    2.723
    /A THR 2085 OG1   /A ARG 2187 HB3    -0.027    2.527
    /A ILE 2084 CD1   /A ILE 2086 CG1    -0.028    3.428
    /A ILE 2079 HG21  /A ILE 2079 HD13   -0.029    2.029
    /A ILE 2084 HD12  /A LEU 2040 HD12   -0.031    2.031
    /A ILE 2025 HG23  /A ILE 2025 HD13   -0.032    2.032
    /A VAL 2057 HG23  /A ASN 2024 CA     -0.037    2.737
    /A LEU 2022 O     /A VAL 2057 H      -0.039    2.059
    /A ILE 2079 O     /A PRO 2182 CD     -0.040    3.160
    /A GLY 2023 O     /A VAL 2057 HG23   -0.045    2.465
    /A GLY 2023 O     /A VAL 2057 HG22   -0.046    2.466
    /A ILE 2025 HB    /A LEU 2022 HD22   -0.047    2.047
    /A ILE 2084 O     /A VAL 2186 HA     -0.047    2.467
    /A ARG 2026 O     /A LEU 1999 HD11   -0.059    2.479
    /A GLY 2023 HA3   /A ALA 2003 HB2    -0.061    2.061
    /A GLU 2021 OE2   /A ARG 2056 NH2    -0.061    2.706
    /A LEU 2022 HD13  /A LEU 2001 HB3    -0.066    2.066
    /A LEU 2041 HD13  /A ASP 2038 HB3    -0.066    2.066
    /A ILE 2079 H     /A LYS 2180 O      -0.068    2.088
    /A ILE 2025 CD1   /A LEU 2040 CD2    -0.069    3.469
    /A ILE 2060 HG21  /A ILE 2060 HD13   -0.076    2.076
    /A GLU 2021 CD    /A ARG 2056 HH11   -0.077    2.957
    /A ARG 2026 HH21  /A GLU 2028 OE1    -0.078    2.098
    /A THR 2085 O     /A LEU 2041 H      -0.080    2.100
    /A ARG 2026 O     /A LEU 1999 HA     -0.082    2.502
    /A ILE 2025 CD1   /A LEU 2040 HD21   -0.085    2.785
    /A ILE 2084 CD1   /A LEU 2040 HD12   -0.085    2.785
    /A ILE 2060 O     /A LEU 2019 HA     -0.089    2.509
    /A ALA 2082 CB    /A VAL 2057 HA     -0.091    2.791
    /A PRO 2058 O     /A GLU 2021 HA     -0.095    2.515
    /A ILE 2025 HA    /A VAL 2000 O      -0.096    2.516
    /A PRO 2058 CD    /A LEU 2022 HB3    -0.097    2.797
    /A LEU 2020 HD21  /A GLU 2021 N      -0.097    2.722
    /A LEU 2020 HB3   /A ILE 2060 HB     -0.100    2.100
    /A ARG 2026 CA    /A LEU 2040 O      -0.102    3.222
    /A ILE 2079 O     /A ILE 2181 HG22   -0.102    2.522
    /A VAL 2081 HB    /A VAL 2184 HG22   -0.103    2.103
    /A LEU 2041 O     /A THR 2085 N      -0.104    2.749
    /A VAL 2057 O     /A VAL 2081 HA     -0.105    2.525
    /A ILE 2079 CD1   /A PHE 2077 CE1    -0.105    3.505
    /A ASN 2080 O     /A PRO 2058 HA     -0.106    2.526
    /A LEU 2041 O     /A ILE 2084 HA     -0.106    2.526
    /A ARG 2059 O     /A ASN 2080 N      -0.107    2.752
    /A ALA 2042 C     /A THR 2043 HG1    -0.108    2.718
    /A VAL 2057 CG1   /A PRO 2058 CG     -0.112    3.512
    /A LEU 2041 CD1   /A ASP 2038 CB     -0.113    3.513
    /A PRO 2058 HD3   /A VAL 2057 CB     -0.115    2.815
    /A ILE 2025 O     /A ILE 2025 HG22   -0.117    2.537
    /A ILE 2025 CG2   /A VAL 2057 CG1    -0.121    3.521
    /A PRO 2083 CD    /A ALA 2082 HB1    -0.122    2.822
    /A THR 2085 OG1   /A THR 2043 CB     -0.122    3.322
    /A THR 2085 OG1   /A THR 2043 HG21   -0.134    2.634
    /A PRO 2058 CG    /A LEU 2022 HD21   -0.135    2.835
    /A LEU 2022 CD2   /A LEU 2001 HD23   -0.135    2.835
    /A ARG 2026 CG    /A LEU 2041 HD22   -0.139    2.839
    /A GLU 2021 O     /A PHE 2004 HA     -0.139    2.559
    /A GLU 2021 CD    /A ARG 2056 CD     -0.141    3.721
    /A LEU 2041 HG    /A LEU 2040 C      -0.142    2.752
    /A ALA 2082 HA    /A PRO 2083 HD2    -0.144    2.144
    /A PRO 2058 HD3   /A LEU 2022 CB     -0.144    2.844
    /A LEU 2020 O     /A ARG 2059 CA     -0.146    3.266
    /A LEU 2022 HD22  /A LEU 2001 HD23   -0.148    2.148
    /A THR 2085 HG1   /A THR 2043 HG1    -0.151    2.151
    /A THR 2085 OG1   /A THR 2043 CG2    -0.155    3.355
    /A VAL 2057 HA    /A ALA 2082 HB2    -0.156    2.156
    /A VAL 2081 HG21  /A ILE 2079 HG23   -0.159    2.159
    /A ILE 2079 HB    /A ILE 2181 HG13   -0.159    2.159
    /A GLU 2021 CD    /A ARG 2056 HH12   -0.159    3.039
    /A PRO 2083 HB3   /A ILE 2045 CG1    -0.161    2.861
    /A ALA 2082 N     /A VAL 2081 HG11   -0.163    2.788
    /A GLY 2023 H     /A SER 2002 O      -0.163    2.183
    /A LEU 2041 O     /A ILE 2084 CA     -0.164    3.284
    /A ARG 2026 O     /A VAL 2000 N      -0.169    2.814
    /A ARG 2026 CG    /A LEU 2041 HD23   -0.169    2.869
    /A LEU 2022 O     /A VAL 2057 N      -0.170    2.815
    /A LEU 2020 O     /A ILE 2060 N      -0.172    2.817
    /A LEU 2020 HA    /A LEU 2005 O      -0.173    2.593
    /A THR 2085 CA    /A ARG 2187 O      -0.173    3.293
    /A LEU 2022 HA    /A LEU 2022 HD11   -0.175    2.175
    /A ILE 2084 HG22  /A PRO 2083 C      -0.176    2.786
    /A GLU 2021 CD    /A ARG 2056 HD3    -0.176    3.056
    /A ILE 2025 H     /A ASN 2024 OD1    -0.178    2.198
    /A ASN 2024 HB3   /A SER 2002 HG     -0.178    2.178
    /A VAL 2081 CG2   /A ILE 2079 HG23   -0.180    2.880
    /A GLU 2021 HB3   /A ARG 2056 HD3    -0.183    2.183
    /A ASN 2024 O     /A SER 2002 H      -0.184    2.204
    /A PRO 2083 CA    /A PRO 2185 O      -0.184    3.304
    /A GLU 2021 N     /A LEU 2005 O      -0.185    2.830
    /A ILE 2060 HG12  /A ILE 2079 HG22   -0.190    2.190
    /A LEU 2020 HD12  /A PHE 2004 HE2    -0.192    2.192
    /A THR 2085 HG1   /A THR 2043 HG21   -0.194    2.194
    /A ILE 2084 HD12  /A ILE 2086 HG12   -0.197    2.197
    /A GLU 2021 OE1   /A ARG 2056 HH12   -0.197    2.217
    /A ILE 2079 CD1   /A PHE 2077 HE1    -0.200    2.900
    /A LEU 2022 CD1   /A LEU 2001 HB3    -0.200    2.900
    /A ILE 2060 CA    /A GLU 2078 O      -0.201    3.321
    /A ILE 2084 CG1   /A VAL 2186 HG11   -0.202    2.902
    /A LEU 2041 HD22  /A LEU 2041 HA     -0.205    2.205
    /A ILE 2025 HG13  /A LEU 2040 HD21   -0.206    2.206
    /A ASN 2024 O     /A LEU 2001 HA     -0.208    2.628
    /A LEU 2020 N     /A ILE 2060 O      -0.212    2.857
    /A VAL 2057 O     /A ALA 2082 N      -0.214    2.859
    /A VAL 2081 HB    /A VAL 2184 CG2    -0.222    2.922
    /A ARG 2026 NH2   /A GLU 2028 CD     -0.223    3.728
    /A ILE 2025 HG12  /A LEU 2001 CD2    -0.223    2.923
    /A GLU 2021 OE2   /A ARG 2056 NH1    -0.226    2.871
    /A ASN 2080 O     /A ARG 2059 N      -0.227    2.872
    /A ILE 2025 CG1   /A LEU 2040 HD21   -0.229    2.929
    /A LEU 2022 HD22  /A LEU 2001 CD2    -0.231    2.931
    /A LEU 2020 HB2   /A TYR 2006 HD2    -0.232    2.232
    /A ILE 2084 CD1   /A LEU 2040 CD1    -0.232    3.632
    /A ASN 2024 OD1   /A ILE 2025 N      -0.233    2.878
    /A GLU 2021 OE1   /A LEU 2019 HD23   -0.237    2.657
    /A ILE 2079 HD11  /A PHE 2077 CZ     -0.239    2.939
    /A ILE 2079 O     /A ILE 2181 HA     -0.241    2.661
    /A ILE 2025 HG12  /A LEU 2001 HD21   -0.241    2.241
    /A ARG 2059 NE    /A LEU 2019 HD13   -0.243    2.868
    /A GLU 2021 HG3   /A LEU 2019 HG     -0.243    2.243
    /A ILE 2084 O     /A VAL 2186 CA     -0.246    3.366
    /A LEU 2041 HG    /A LEU 2040 O      -0.249    2.669
    /A ILE 2084 HD13  /A ILE 2086 CD1    -0.250    2.950
    /A ALA 2082 HB1   /A PRO 2083 HD3    -0.251    2.251
    /A ILE 2084 HD12  /A ILE 2086 CD1    -0.251    2.951
    /A ARG 2059 O     /A ILE 2079 HA     -0.253    2.673
    /A LEU 2020 CD2   /A GLU 2021 N      -0.254    3.579
    /A LEU 2041 CD2   /A ARG 2026 CD     -0.255    3.655
    /A ARG 2026 HH21  /A GLU 2028 CD     -0.261    3.141
    /A ILE 2084 HG13  /A ILE 2086 HG13   -0.261    2.261
    /A LEU 2041 CD1   /A ASP 2038 CG     -0.261    3.841
    /A LEU 2041 CG    /A LEU 2040 O      -0.262    3.382
    /A THR 2085 O     /A LEU 2040 CA     -0.262    3.382
    /A GLU 2021 HG2   /A ARG 2059 HG3    -0.264    2.264
    /A PRO 2083 CB    /A THR 2043 O      -0.268    3.388
    /A PRO 2058 O     /A LEU 2022 N      -0.268    2.913
    /A ILE 2025 CG1   /A LEU 1999 HD13   -0.269    2.969
    /A ASN 2024 CG    /A ILE 2025 H      -0.272    2.882
    /A GLU 2021 CD    /A LEU 2019 HD23   -0.273    3.153
    /A GLY 2023 CA    /A SER 2002 O      -0.273    3.393
    /A LEU 2022 HD13  /A LEU 2001 CB     -0.274    2.974
    /A VAL 2081 CG1   /A ALA 2082 O      -0.274    3.394
    /A LEU 2022 O     /A PRO 2058 HD3    -0.277    2.697
    /A ARG 2026 HD3   /A ARG 2026 HH11   -0.280    2.280
    /A PRO 2083 CB    /A ILE 2045 CG1    -0.282    3.682
    /A LEU 2022 O     /A PRO 2058 CD     -0.283    3.403
    /A GLU 2021 OE1   /A ARG 2056 HH11   -0.284    2.304
    /A VAL 2081 O     /A VAL 2184 HG23   -0.284    2.704
    /A LEU 2022 O     /A PRO 2058 N      -0.286    3.346
    /A LEU 2022 HD12  /A PHE 2004 HD2    -0.289    2.289
    /A PRO 2083 CG    /A ILE 2045 HD12   -0.289    2.989
    /A ARG 2026 HB3   /A VAL 2000 HB     -0.290    2.290
    /A THR 2085 HG23  /A ILE 2086 N      -0.291    2.916
    /A LEU 2020 C     /A GLU 2021 HG3    -0.291    2.901
    /A ASN 2080 ND2   /A GLU 2078 HG3    -0.292    2.917
    /A ILE 2084 HG12  /A VAL 2186 HG11   -0.292    2.292
    /A LEU 2022 CD2   /A PRO 2058 HG3    -0.297    2.997
    /A ILE 2079 N     /A GLU 2078 HG3    -0.298    2.923
    /A THR 2085 HA    /A ARG 2187 HB3    -0.302    2.302
    /A VAL 2057 C     /A ALA 2082 H      -0.307    2.917
    /A ASN 2024 CB    /A SER 2002 HG     -0.308    3.008
    /A LEU 2020 HD21  /A LEU 2020 O      -0.308    2.728
    /A ARG 2026 O     /A LEU 1999 CA     -0.309    3.429
    /A LEU 2041 O     /A THR 2043 HG1    -0.310    2.330
    /A ILE 2025 CD1   /A LEU 1999 HD13   -0.311    3.011
    /A ILE 2084 O     /A ARG 2187 N      -0.312    2.957
    /A ASN 2080 ND2   /A GLU 2078 OE1    -0.313    2.958
    /A GLY 2023 N     /A SER 2002 O      -0.315    2.960
    /A LEU 2041 HD23  /A ARG 2026 CD     -0.316    3.016
    /A LEU 2020 CD1   /A PHE 2004 HE2    -0.318    3.018
    /A ILE 2060 HG23  /A PHE 2061 N      -0.321    2.946
    /A VAL 2081 O     /A VAL 2184 HG13   -0.322    2.742
    /A ARG 2026 HG2   /A MET 2027 N      -0.325    2.950
    /A ILE 2060 O     /A LEU 2019 CA     -0.325    3.445
    /A GLY 2023 CA    /A ALA 2003 HB2    -0.326    3.026
    /A PRO 2083 CB    /A ILE 2045 HG13   -0.326    3.026
    /A THR 2085 OG1   /A ARG 2187 CB     -0.327    3.527
    /A ASN 2080 C     /A VAL 2081 HG21   -0.327    2.937
    /A PRO 2083 CG    /A ILE 2045 CD1    -0.330    3.730
    /A ASN 2024 H     /A SER 2002 O      -0.334    2.354
    /A VAL 2057 O     /A VAL 2081 CA     -0.336    3.456
    /A ILE 2084 CG2   /A PRO 2083 O      -0.337    3.457
    /A ILE 2079 CG1   /A PHE 2077 CE1    -0.339    3.739
    /A GLU 2021 CA    /A PRO 2058 O      -0.342    3.462
    /A ARG 2059 NE    /A LEU 2019 CD1    -0.342    3.667
    /A LEU 2041 HD23  /A ARG 2026 NE     -0.343    2.968
    /A PRO 2058 CA    /A ASN 2080 O      -0.344    3.464
    /A LEU 2020 C     /A ILE 2060 H      -0.344    2.954
    /A ARG 2026 N     /A ILE 2025 HG13   -0.346    2.971
    /A ALA 2042 CB    /A VAL 2057 HG21   -0.353    3.053
    /A LEU 2022 HD11  /A SER 2002 O      -0.353    2.773
    /A PRO 2083 O     /A THR 2043 N      -0.353    2.998
    /A LEU 2022 HB3   /A PRO 2058 HB2    -0.354    2.354
    /A PRO 2058 CD    /A LEU 2022 HD21   -0.357    3.057
    /A LEU 2022 O     /A ARG 2056 CA     -0.358    3.478
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.361    3.061
    /A ARG 2059 C     /A ASN 2080 H      -0.361    2.971
    /A ARG 2026 N     /A VAL 2000 O      -0.361    3.006
    /A ILE 2060 CG2   /A PHE 2077 CE2    -0.363    3.763
    /A LEU 2041 CG    /A ASP 2038 HB3    -0.363    3.063
    /A ARG 2059 CB    /A ASN 2080 HB3    -0.365    3.065
    /A ILE 2079 HG13  /A ILE 2060 HG22   -0.365    2.365
    /A ILE 2025 CB    /A LEU 2022 HD22   -0.366    3.066
    /A GLY 2023 N     /A LEU 2022 HG     -0.366    2.991
    /A GLU 2021 CB    /A ARG 2056 HD3    -0.366    3.066
    /A THR 2085 C     /A ILE 2086 HG13   -0.367    2.977
    /A ASN 2080 ND2   /A GLU 2078 CG     -0.367    3.692
    /A VAL 2057 CB    /A PRO 2058 CG     -0.369    3.769
    /A VAL 2057 CG2   /A ASN 2024 CA     -0.369    3.769
    /A ASN 2080 OD1   /A GLU 2078 OE1    -0.371    3.211
    /A LEU 2041 C     /A THR 2085 H      -0.373    2.983
    /A GLU 2021 O     /A LEU 2005 N      -0.373    3.018
    /A GLU 2021 OE2   /A ARG 2056 NE     -0.374    3.019
    /A ILE 2025 CA    /A VAL 2000 O      -0.375    3.495
    /A ASN 2080 CB    /A ARG 2059 HB3    -0.377    3.077
    /A ILE 2025 CG1   /A LEU 2001 CD2    -0.385    3.785
    /A LEU 2022 CD2   /A LEU 2001 CD2    -0.386    3.786
    /A ILE 2060 O     /A LEU 2019 HD11   -0.388    2.808
    /A ILE 2079 HD12  /A ILE 2181 CD1    -0.389    3.089
    /A ILE 2025 HD12  /A LEU 2040 HD21   -0.390    2.390
    /A ILE 2084 H     /A ILE 2084 HG12   -0.390    2.390
    /A ILE 2079 O     /A ILE 2181 CG2    -0.390    3.510
    /A PRO 2058 CD    /A LEU 2022 CB     -0.391    3.791
    /A ILE 2084 CG1   /A ILE 2086 HG13   -0.391    3.091
    /A THR 2085 OG1   /A ARG 2187 HD2    -0.392    2.892
    /A ILE 2025 HD13  /A LEU 2040 CD2    -0.392    3.092
    /A LEU 2041 HB2   /A THR 2085 HB     -0.392    2.392
    /A ILE 2025 HD12  /A LEU 2040 CD2    -0.392    3.092
    /A VAL 2057 O     /A PRO 2058 HG2    -0.393    2.813
    /A LEU 2020 O     /A GLU 2021 CG     -0.393    3.513
    /A ARG 2026 C     /A VAL 2000 H      -0.393    3.003
    /A ILE 2025 HG12  /A LEU 1999 HD13   -0.394    2.394
    /A ASN 2080 OD1   /A PRO 2182 CD     -0.395    3.515
    /A ILE 2079 N     /A LYS 2180 O      -0.399    3.044
    /A THR 2085 N     /A THR 2043 OG1    -0.399    3.124
    /A PRO 2058 CG    /A LEU 2022 HB3    -0.400    3.100
    

  
323 contacts  

> ui tool show Contacts

> close #1.1

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel intraRes true ignoreHiddenModels true color #ffffff dashes 4
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    323 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 CB    /A PRO 2058 HD2    1.082    1.618
    /A VAL 2057 CG1   /A PRO 2058 HD2    0.984    1.716
    /A GLU 2021 CD    /A ARG 2056 NH1    0.716    2.789
    /A PRO 2083 HB3   /A ILE 2045 HD12   0.629    1.371
    /A PRO 2058 CD    /A VAL 2057 HB     0.618    2.082
    /A PRO 2058 CD    /A VAL 2057 CG1    0.603    2.797
    /A THR 2085 HG1   /A THR 2043 OG1    0.505    1.595
    /A GLU 2021 CD    /A ARG 2056 CZ     0.496    2.994
    /A PRO 2058 HD2   /A VAL 2057 HB     0.482    1.518
    /A GLU 2021 OE2   /A ARG 2056 CZ     0.469    2.561
    /A ALA 2082 O     /A ILE 2084 HG22   0.435    1.985
    /A GLU 2021 OE1   /A ARG 2056 NH1    0.430    2.215
    /A ASN 2080 OD1   /A PRO 2182 HG2    0.403    2.017
    /A PRO 2083 HB3   /A ILE 2045 CD1    0.352    2.348
    /A VAL 2057 HG23  /A ASN 2024 HA     0.336    1.664
    /A VAL 2057 HG12  /A ILE 2025 HG21   0.327    1.673
    /A ASN 2024 HB3   /A SER 2002 OG     0.311    2.189
    /A PRO 2083 CB    /A ILE 2045 HD12   0.299    2.401
    /A LEU 2041 CD2   /A ARG 2026 HG3    0.297    2.403
    /A THR 2085 HG1   /A THR 2043 CB     0.286    2.414
    /A ASN 2080 HD22  /A GLU 2078 CD     0.273    2.607
    /A ASN 2080 H     /A ARG 2059 O      0.258    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.249    2.871
    /A THR 2085 H     /A LEU 2041 O      0.230    1.790
    /A ARG 2026 O     /A VAL 2000 H      0.204    1.816
    /A VAL 2057 HG13  /A PRO 2058 HD2    0.201    1.799
    /A ILE 2060 H     /A LEU 2020 O      0.195    1.825
    /A VAL 2057 HG12  /A PRO 2058 HD2    0.194    1.806
    /A ILE 2025 CG2   /A VAL 2057 HG12   0.191    2.509
    /A ARG 2026 HA    /A LEU 2040 O      0.189    2.231
    /A GLU 2021 H     /A LEU 2005 O      0.173    1.847
    /A ILE 2060 O     /A LEU 2020 H      0.170    1.850
    /A ALA 2082 H     /A VAL 2057 O      0.168    1.852
    /A VAL 2057 O     /A VAL 2057 HG13   0.156    2.264
    /A ILE 2084 HG21  /A ILE 2084 HD11   0.156    1.844
    /A ASN 2080 O     /A ARG 2059 H      0.148    1.872
    /A ASN 2024 CB    /A SER 2002 OG     0.136    3.064
    /A LEU 2020 O     /A ARG 2059 HA     0.122    2.298
    /A ARG 2059 HE    /A LEU 2019 HD13   0.121    1.879
    /A ILE 2079 O     /A PRO 2182 HD3    0.120    2.300
    /A ARG 2026 NH2   /A GLU 2028 OE1    0.119    2.526
    /A ALA 2082 O     /A VAL 2081 HG11   0.113    2.307
    /A PRO 2083 HB2   /A THR 2043 O      0.108    2.312
    /A LEU 2020 C     /A LEU 2020 HD21   0.098    2.512
    /A ASN 2080 OD1   /A PRO 2182 CG     0.098    3.022
    /A LEU 2041 HD13  /A ASP 2038 CG     0.096    2.784
    /A ILE 2079 HD11  /A PHE 2077 CE1    0.091    2.609
    /A ILE 2084 O     /A ILE 2084 HG13   0.085    2.335
    /A PRO 2083 CB    /A ILE 2045 CD1    0.084    3.316
    /A GLU 2021 OE1   /A ARG 2056 CZ     0.084    2.946
    /A THR 2085 H     /A THR 2043 HG1    0.084    1.916
    /A VAL 2057 CG1   /A ILE 2025 HG21   0.083    2.617
    /A PRO 2083 HA    /A PRO 2185 O      0.076    2.344
    /A ALA 2082 O     /A ILE 2084 CG2    0.072    3.048
    /A ARG 2026 CG    /A LEU 2041 CD2    0.064    3.336
    /A THR 2085 OG1   /A THR 2043 OG1    0.058    2.542
    /A ILE 2060 HA    /A GLU 2078 O      0.053    2.367
    /A PRO 2058 HG3   /A LEU 2022 HD21   0.053    1.947
    /A GLU 2021 CD    /A ARG 2056 NE     0.052    3.453
    /A THR 2085 HA    /A ARG 2187 O      0.051    2.369
    /A ARG 2059 HD2   /A ARG 2059 HH11   0.047    1.953
    /A ILE 2084 O     /A ARG 2187 H      0.043    1.977
    /A THR 2085 HG1   /A THR 2043 CG2    0.042    2.658
    /A THR 2085 CB    /A THR 2043 OG1    0.038    3.162
    /A ILE 2084 HD12  /A ILE 2086 CG1    0.027    2.673
    /A THR 2085 O     /A LEU 2040 HA     0.026    2.394
    /A PRO 2058 HD3   /A LEU 2022 HB3    0.025    1.975
    /A PRO 2083 O     /A THR 2043 H      0.023    1.997
    /A ARG 2026 CZ    /A GLU 2028 OE1    0.021    3.009
    /A PRO 2058 O     /A LEU 2022 H      0.018    2.002
    /A ILE 2084 CD1   /A ILE 2086 CD1    0.015    3.385
    /A PRO 2058 HD3   /A VAL 2057 HB     0.015    1.985
    /A LEU 2041 HD23  /A ARG 2026 HG3    0.013    1.987
    /A ILE 2079 HD11  /A PHE 2077 HE1    0.013    1.987
    /A LEU 2041 HD22  /A ARG 2026 HG3    0.013    1.987
    /A ASN 2080 ND2   /A GLU 2078 CD     0.011    3.494
    /A THR 2085 N     /A THR 2043 HG1    0.011    2.614
    /A GLU 2021 CD    /A ARG 2056 NH2    0.010    3.495
    /A ARG 2059 HE    /A LEU 2019 CD1    0.010    2.690
    /A ILE 2084 HD12  /A LEU 2040 CD1    0.009    2.691
    /A GLU 2021 O     /A LEU 2005 H      0.008    2.012
    /A LEU 2041 CD1   /A ASP 2038 HB3    0.006    2.694
    /A LEU 2041 HD13  /A ASP 2038 CB     -0.001    2.701
    /A ASN 2080 HD22  /A GLU 2078 OE1    -0.004    2.024
    /A ASN 2080 HB3   /A ARG 2059 HB3    -0.009    2.009
    /A PRO 2058 CD    /A VAL 2057 HG13   -0.013    2.713
    /A PRO 2058 CD    /A VAL 2057 HG12   -0.013    2.713
    /A VAL 2057 CG2   /A ASN 2024 HA     -0.023    2.723
    /A ARG 2026 H     /A VAL 2000 O      -0.023    2.043
    /A LEU 2022 CD2   /A ILE 2025 HB     -0.023    2.723
    /A THR 2085 OG1   /A ARG 2187 HB3    -0.027    2.527
    /A ILE 2084 CD1   /A ILE 2086 CG1    -0.028    3.428
    /A ILE 2079 HG21  /A ILE 2079 HD13   -0.029    2.029
    /A ILE 2084 HD12  /A LEU 2040 HD12   -0.031    2.031
    /A ILE 2025 HG23  /A ILE 2025 HD13   -0.032    2.032
    /A VAL 2057 HG23  /A ASN 2024 CA     -0.037    2.737
    /A LEU 2022 O     /A VAL 2057 H      -0.039    2.059
    /A ILE 2079 O     /A PRO 2182 CD     -0.040    3.160
    /A GLY 2023 O     /A VAL 2057 HG23   -0.045    2.465
    /A GLY 2023 O     /A VAL 2057 HG22   -0.046    2.466
    /A ILE 2025 HB    /A LEU 2022 HD22   -0.047    2.047
    /A ILE 2084 O     /A VAL 2186 HA     -0.047    2.467
    /A ARG 2026 O     /A LEU 1999 HD11   -0.059    2.479
    /A GLY 2023 HA3   /A ALA 2003 HB2    -0.061    2.061
    /A GLU 2021 OE2   /A ARG 2056 NH2    -0.061    2.706
    /A LEU 2022 HD13  /A LEU 2001 HB3    -0.066    2.066
    /A LEU 2041 HD13  /A ASP 2038 HB3    -0.066    2.066
    /A ILE 2079 H     /A LYS 2180 O      -0.068    2.088
    /A ILE 2025 CD1   /A LEU 2040 CD2    -0.069    3.469
    /A ILE 2060 HG21  /A ILE 2060 HD13   -0.076    2.076
    /A GLU 2021 CD    /A ARG 2056 HH11   -0.077    2.957
    /A ARG 2026 HH21  /A GLU 2028 OE1    -0.078    2.098
    /A THR 2085 O     /A LEU 2041 H      -0.080    2.100
    /A ARG 2026 O     /A LEU 1999 HA     -0.082    2.502
    /A ILE 2025 CD1   /A LEU 2040 HD21   -0.085    2.785
    /A ILE 2084 CD1   /A LEU 2040 HD12   -0.085    2.785
    /A ILE 2060 O     /A LEU 2019 HA     -0.089    2.509
    /A ALA 2082 CB    /A VAL 2057 HA     -0.091    2.791
    /A PRO 2058 O     /A GLU 2021 HA     -0.095    2.515
    /A ILE 2025 HA    /A VAL 2000 O      -0.096    2.516
    /A PRO 2058 CD    /A LEU 2022 HB3    -0.097    2.797
    /A LEU 2020 HD21  /A GLU 2021 N      -0.097    2.722
    /A LEU 2020 HB3   /A ILE 2060 HB     -0.100    2.100
    /A ARG 2026 CA    /A LEU 2040 O      -0.102    3.222
    /A ILE 2079 O     /A ILE 2181 HG22   -0.102    2.522
    /A VAL 2081 HB    /A VAL 2184 HG22   -0.103    2.103
    /A LEU 2041 O     /A THR 2085 N      -0.104    2.749
    /A VAL 2057 O     /A VAL 2081 HA     -0.105    2.525
    /A ILE 2079 CD1   /A PHE 2077 CE1    -0.105    3.505
    /A ASN 2080 O     /A PRO 2058 HA     -0.106    2.526
    /A LEU 2041 O     /A ILE 2084 HA     -0.106    2.526
    /A ARG 2059 O     /A ASN 2080 N      -0.107    2.752
    /A ALA 2042 C     /A THR 2043 HG1    -0.108    2.718
    /A VAL 2057 CG1   /A PRO 2058 CG     -0.112    3.512
    /A LEU 2041 CD1   /A ASP 2038 CB     -0.113    3.513
    /A PRO 2058 HD3   /A VAL 2057 CB     -0.115    2.815
    /A ILE 2025 O     /A ILE 2025 HG22   -0.117    2.537
    /A ILE 2025 CG2   /A VAL 2057 CG1    -0.121    3.521
    /A PRO 2083 CD    /A ALA 2082 HB1    -0.122    2.822
    /A THR 2085 OG1   /A THR 2043 CB     -0.122    3.322
    /A THR 2085 OG1   /A THR 2043 HG21   -0.134    2.634
    /A PRO 2058 CG    /A LEU 2022 HD21   -0.135    2.835
    /A LEU 2022 CD2   /A LEU 2001 HD23   -0.135    2.835
    /A ARG 2026 CG    /A LEU 2041 HD22   -0.139    2.839
    /A GLU 2021 O     /A PHE 2004 HA     -0.139    2.559
    /A GLU 2021 CD    /A ARG 2056 CD     -0.141    3.721
    /A LEU 2041 HG    /A LEU 2040 C      -0.142    2.752
    /A ALA 2082 HA    /A PRO 2083 HD2    -0.144    2.144
    /A PRO 2058 HD3   /A LEU 2022 CB     -0.144    2.844
    /A LEU 2020 O     /A ARG 2059 CA     -0.146    3.266
    /A LEU 2022 HD22  /A LEU 2001 HD23   -0.148    2.148
    /A THR 2085 HG1   /A THR 2043 HG1    -0.151    2.151
    /A THR 2085 OG1   /A THR 2043 CG2    -0.155    3.355
    /A VAL 2057 HA    /A ALA 2082 HB2    -0.156    2.156
    /A VAL 2081 HG21  /A ILE 2079 HG23   -0.159    2.159
    /A ILE 2079 HB    /A ILE 2181 HG13   -0.159    2.159
    /A GLU 2021 CD    /A ARG 2056 HH12   -0.159    3.039
    /A PRO 2083 HB3   /A ILE 2045 CG1    -0.161    2.861
    /A ALA 2082 N     /A VAL 2081 HG11   -0.163    2.788
    /A GLY 2023 H     /A SER 2002 O      -0.163    2.183
    /A LEU 2041 O     /A ILE 2084 CA     -0.164    3.284
    /A ARG 2026 O     /A VAL 2000 N      -0.169    2.814
    /A ARG 2026 CG    /A LEU 2041 HD23   -0.169    2.869
    /A LEU 2022 O     /A VAL 2057 N      -0.170    2.815
    /A LEU 2020 O     /A ILE 2060 N      -0.172    2.817
    /A LEU 2020 HA    /A LEU 2005 O      -0.173    2.593
    /A THR 2085 CA    /A ARG 2187 O      -0.173    3.293
    /A LEU 2022 HA    /A LEU 2022 HD11   -0.175    2.175
    /A ILE 2084 HG22  /A PRO 2083 C      -0.176    2.786
    /A GLU 2021 CD    /A ARG 2056 HD3    -0.176    3.056
    /A ILE 2025 H     /A ASN 2024 OD1    -0.178    2.198
    /A ASN 2024 HB3   /A SER 2002 HG     -0.178    2.178
    /A VAL 2081 CG2   /A ILE 2079 HG23   -0.180    2.880
    /A GLU 2021 HB3   /A ARG 2056 HD3    -0.183    2.183
    /A ASN 2024 O     /A SER 2002 H      -0.184    2.204
    /A PRO 2083 CA    /A PRO 2185 O      -0.184    3.304
    /A GLU 2021 N     /A LEU 2005 O      -0.185    2.830
    /A ILE 2060 HG12  /A ILE 2079 HG22   -0.190    2.190
    /A LEU 2020 HD12  /A PHE 2004 HE2    -0.192    2.192
    /A THR 2085 HG1   /A THR 2043 HG21   -0.194    2.194
    /A ILE 2084 HD12  /A ILE 2086 HG12   -0.197    2.197
    /A GLU 2021 OE1   /A ARG 2056 HH12   -0.197    2.217
    /A ILE 2079 CD1   /A PHE 2077 HE1    -0.200    2.900
    /A LEU 2022 CD1   /A LEU 2001 HB3    -0.200    2.900
    /A ILE 2060 CA    /A GLU 2078 O      -0.201    3.321
    /A ILE 2084 CG1   /A VAL 2186 HG11   -0.202    2.902
    /A LEU 2041 HD22  /A LEU 2041 HA     -0.205    2.205
    /A ILE 2025 HG13  /A LEU 2040 HD21   -0.206    2.206
    /A ASN 2024 O     /A LEU 2001 HA     -0.208    2.628
    /A LEU 2020 N     /A ILE 2060 O      -0.212    2.857
    /A VAL 2057 O     /A ALA 2082 N      -0.214    2.859
    /A VAL 2081 HB    /A VAL 2184 CG2    -0.222    2.922
    /A ARG 2026 NH2   /A GLU 2028 CD     -0.223    3.728
    /A ILE 2025 HG12  /A LEU 2001 CD2    -0.223    2.923
    /A GLU 2021 OE2   /A ARG 2056 NH1    -0.226    2.871
    /A ASN 2080 O     /A ARG 2059 N      -0.227    2.872
    /A ILE 2025 CG1   /A LEU 2040 HD21   -0.229    2.929
    /A LEU 2022 HD22  /A LEU 2001 CD2    -0.231    2.931
    /A LEU 2020 HB2   /A TYR 2006 HD2    -0.232    2.232
    /A ILE 2084 CD1   /A LEU 2040 CD1    -0.232    3.632
    /A ASN 2024 OD1   /A ILE 2025 N      -0.233    2.878
    /A GLU 2021 OE1   /A LEU 2019 HD23   -0.237    2.657
    /A ILE 2079 HD11  /A PHE 2077 CZ     -0.239    2.939
    /A ILE 2079 O     /A ILE 2181 HA     -0.241    2.661
    /A ILE 2025 HG12  /A LEU 2001 HD21   -0.241    2.241
    /A ARG 2059 NE    /A LEU 2019 HD13   -0.243    2.868
    /A GLU 2021 HG3   /A LEU 2019 HG     -0.243    2.243
    /A ILE 2084 O     /A VAL 2186 CA     -0.246    3.366
    /A LEU 2041 HG    /A LEU 2040 O      -0.249    2.669
    /A ILE 2084 HD13  /A ILE 2086 CD1    -0.250    2.950
    /A ALA 2082 HB1   /A PRO 2083 HD3    -0.251    2.251
    /A ILE 2084 HD12  /A ILE 2086 CD1    -0.251    2.951
    /A ARG 2059 O     /A ILE 2079 HA     -0.253    2.673
    /A LEU 2020 CD2   /A GLU 2021 N      -0.254    3.579
    /A LEU 2041 CD2   /A ARG 2026 CD     -0.255    3.655
    /A ARG 2026 HH21  /A GLU 2028 CD     -0.261    3.141
    /A ILE 2084 HG13  /A ILE 2086 HG13   -0.261    2.261
    /A LEU 2041 CD1   /A ASP 2038 CG     -0.261    3.841
    /A LEU 2041 CG    /A LEU 2040 O      -0.262    3.382
    /A THR 2085 O     /A LEU 2040 CA     -0.262    3.382
    /A GLU 2021 HG2   /A ARG 2059 HG3    -0.264    2.264
    /A PRO 2083 CB    /A THR 2043 O      -0.268    3.388
    /A PRO 2058 O     /A LEU 2022 N      -0.268    2.913
    /A ILE 2025 CG1   /A LEU 1999 HD13   -0.269    2.969
    /A ASN 2024 CG    /A ILE 2025 H      -0.272    2.882
    /A GLU 2021 CD    /A LEU 2019 HD23   -0.273    3.153
    /A GLY 2023 CA    /A SER 2002 O      -0.273    3.393
    /A LEU 2022 HD13  /A LEU 2001 CB     -0.274    2.974
    /A VAL 2081 CG1   /A ALA 2082 O      -0.274    3.394
    /A LEU 2022 O     /A PRO 2058 HD3    -0.277    2.697
    /A ARG 2026 HD3   /A ARG 2026 HH11   -0.280    2.280
    /A PRO 2083 CB    /A ILE 2045 CG1    -0.282    3.682
    /A LEU 2022 O     /A PRO 2058 CD     -0.283    3.403
    /A GLU 2021 OE1   /A ARG 2056 HH11   -0.284    2.304
    /A VAL 2081 O     /A VAL 2184 HG23   -0.284    2.704
    /A LEU 2022 O     /A PRO 2058 N      -0.286    3.346
    /A LEU 2022 HD12  /A PHE 2004 HD2    -0.289    2.289
    /A PRO 2083 CG    /A ILE 2045 HD12   -0.289    2.989
    /A ARG 2026 HB3   /A VAL 2000 HB     -0.290    2.290
    /A THR 2085 HG23  /A ILE 2086 N      -0.291    2.916
    /A LEU 2020 C     /A GLU 2021 HG3    -0.291    2.901
    /A ASN 2080 ND2   /A GLU 2078 HG3    -0.292    2.917
    /A ILE 2084 HG12  /A VAL 2186 HG11   -0.292    2.292
    /A LEU 2022 CD2   /A PRO 2058 HG3    -0.297    2.997
    /A ILE 2079 N     /A GLU 2078 HG3    -0.298    2.923
    /A THR 2085 HA    /A ARG 2187 HB3    -0.302    2.302
    /A VAL 2057 C     /A ALA 2082 H      -0.307    2.917
    /A ASN 2024 CB    /A SER 2002 HG     -0.308    3.008
    /A LEU 2020 HD21  /A LEU 2020 O      -0.308    2.728
    /A ARG 2026 O     /A LEU 1999 CA     -0.309    3.429
    /A LEU 2041 O     /A THR 2043 HG1    -0.310    2.330
    /A ILE 2025 CD1   /A LEU 1999 HD13   -0.311    3.011
    /A ILE 2084 O     /A ARG 2187 N      -0.312    2.957
    /A ASN 2080 ND2   /A GLU 2078 OE1    -0.313    2.958
    /A GLY 2023 N     /A SER 2002 O      -0.315    2.960
    /A LEU 2041 HD23  /A ARG 2026 CD     -0.316    3.016
    /A LEU 2020 CD1   /A PHE 2004 HE2    -0.318    3.018
    /A ILE 2060 HG23  /A PHE 2061 N      -0.321    2.946
    /A VAL 2081 O     /A VAL 2184 HG13   -0.322    2.742
    /A ARG 2026 HG2   /A MET 2027 N      -0.325    2.950
    /A ILE 2060 O     /A LEU 2019 CA     -0.325    3.445
    /A GLY 2023 CA    /A ALA 2003 HB2    -0.326    3.026
    /A PRO 2083 CB    /A ILE 2045 HG13   -0.326    3.026
    /A THR 2085 OG1   /A ARG 2187 CB     -0.327    3.527
    /A ASN 2080 C     /A VAL 2081 HG21   -0.327    2.937
    /A PRO 2083 CG    /A ILE 2045 CD1    -0.330    3.730
    /A ASN 2024 H     /A SER 2002 O      -0.334    2.354
    /A VAL 2057 O     /A VAL 2081 CA     -0.336    3.456
    /A ILE 2084 CG2   /A PRO 2083 O      -0.337    3.457
    /A ILE 2079 CG1   /A PHE 2077 CE1    -0.339    3.739
    /A GLU 2021 CA    /A PRO 2058 O      -0.342    3.462
    /A ARG 2059 NE    /A LEU 2019 CD1    -0.342    3.667
    /A LEU 2041 HD23  /A ARG 2026 NE     -0.343    2.968
    /A PRO 2058 CA    /A ASN 2080 O      -0.344    3.464
    /A LEU 2020 C     /A ILE 2060 H      -0.344    2.954
    /A ARG 2026 N     /A ILE 2025 HG13   -0.346    2.971
    /A ALA 2042 CB    /A VAL 2057 HG21   -0.353    3.053
    /A LEU 2022 HD11  /A SER 2002 O      -0.353    2.773
    /A PRO 2083 O     /A THR 2043 N      -0.353    2.998
    /A LEU 2022 HB3   /A PRO 2058 HB2    -0.354    2.354
    /A PRO 2058 CD    /A LEU 2022 HD21   -0.357    3.057
    /A LEU 2022 O     /A ARG 2056 CA     -0.358    3.478
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.361    3.061
    /A ARG 2059 C     /A ASN 2080 H      -0.361    2.971
    /A ARG 2026 N     /A VAL 2000 O      -0.361    3.006
    /A ILE 2060 CG2   /A PHE 2077 CE2    -0.363    3.763
    /A LEU 2041 CG    /A ASP 2038 HB3    -0.363    3.063
    /A ARG 2059 CB    /A ASN 2080 HB3    -0.365    3.065
    /A ILE 2079 HG13  /A ILE 2060 HG22   -0.365    2.365
    /A ILE 2025 CB    /A LEU 2022 HD22   -0.366    3.066
    /A GLY 2023 N     /A LEU 2022 HG     -0.366    2.991
    /A GLU 2021 CB    /A ARG 2056 HD3    -0.366    3.066
    /A THR 2085 C     /A ILE 2086 HG13   -0.367    2.977
    /A ASN 2080 ND2   /A GLU 2078 CG     -0.367    3.692
    /A VAL 2057 CB    /A PRO 2058 CG     -0.369    3.769
    /A VAL 2057 CG2   /A ASN 2024 CA     -0.369    3.769
    /A ASN 2080 OD1   /A GLU 2078 OE1    -0.371    3.211
    /A LEU 2041 C     /A THR 2085 H      -0.373    2.983
    /A GLU 2021 O     /A LEU 2005 N      -0.373    3.018
    /A GLU 2021 OE2   /A ARG 2056 NE     -0.374    3.019
    /A ILE 2025 CA    /A VAL 2000 O      -0.375    3.495
    /A ASN 2080 CB    /A ARG 2059 HB3    -0.377    3.077
    /A ILE 2025 CG1   /A LEU 2001 CD2    -0.385    3.785
    /A LEU 2022 CD2   /A LEU 2001 CD2    -0.386    3.786
    /A ILE 2060 O     /A LEU 2019 HD11   -0.388    2.808
    /A ILE 2079 HD12  /A ILE 2181 CD1    -0.389    3.089
    /A ILE 2025 HD12  /A LEU 2040 HD21   -0.390    2.390
    /A ILE 2084 H     /A ILE 2084 HG12   -0.390    2.390
    /A ILE 2079 O     /A ILE 2181 CG2    -0.390    3.510
    /A PRO 2058 CD    /A LEU 2022 CB     -0.391    3.791
    /A ILE 2084 CG1   /A ILE 2086 HG13   -0.391    3.091
    /A THR 2085 OG1   /A ARG 2187 HD2    -0.392    2.892
    /A ILE 2025 HD13  /A LEU 2040 CD2    -0.392    3.092
    /A LEU 2041 HB2   /A THR 2085 HB     -0.392    2.392
    /A ILE 2025 HD12  /A LEU 2040 CD2    -0.392    3.092
    /A VAL 2057 O     /A PRO 2058 HG2    -0.393    2.813
    /A LEU 2020 O     /A GLU 2021 CG     -0.393    3.513
    /A ARG 2026 C     /A VAL 2000 H      -0.393    3.003
    /A ILE 2025 HG12  /A LEU 1999 HD13   -0.394    2.394
    /A ASN 2080 OD1   /A PRO 2182 CD     -0.395    3.515
    /A ILE 2079 N     /A LYS 2180 O      -0.399    3.044
    /A THR 2085 N     /A THR 2043 OG1    -0.399    3.124
    /A PRO 2058 CG    /A LEU 2022 HB3    -0.400    3.100
    

  
323 contacts  

> close #1.1

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> select clear

> select /A:2020-2027

134 atoms, 133 bonds, 8 residues, 1 model selected  

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 20 residues, 1 model selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 4 pseudobonds, 20 residues, 2 models selected  

> close #1.1

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    130 contacts
         atom1             atom2        overlap  distance
    /A PRO 2058 HD2   /A VAL 2057 CB     1.082    1.618
    /A PRO 2058 HD2   /A VAL 2057 CG1    0.984    1.716
    /A VAL 2057 HB    /A PRO 2058 CD     0.618    2.082
    /A VAL 2057 CG1   /A PRO 2058 CD     0.603    2.797
    /A VAL 2057 HB    /A PRO 2058 HD2    0.482    1.518
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A PRO 2058 HD2   /A VAL 2057 HG13   0.201    1.799
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A PRO 2058 HD2   /A VAL 2057 HG12   0.194    1.806
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2022 HD21  /A PRO 2058 HG3    0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HB3   /A PRO 2058 HD3    0.025    1.975
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A VAL 2057 HB    /A PRO 2058 HD3    0.015    1.985
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A VAL 2057 HG13  /A PRO 2058 CD     -0.013    2.713
    /A VAL 2057 HG12  /A PRO 2058 CD     -0.013    2.713
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A LEU 2022 HB3   /A PRO 2058 CD     -0.097    2.797
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A PRO 2058 CG    /A VAL 2057 CG1    -0.112    3.512
    /A VAL 2057 CB    /A PRO 2058 HD3    -0.115    2.815
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2022 HD21  /A PRO 2058 CG     -0.135    2.835
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A LEU 2022 CB    /A PRO 2058 HD3    -0.144    2.844
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A PRO 2058 HD3   /A LEU 2022 O      -0.277    2.697
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A PRO 2058 CD    /A LEU 2022 O      -0.283    3.403
    /A PRO 2058 N     /A LEU 2022 O      -0.286    3.346
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 HG3   /A LEU 2022 CD2    -0.297    2.997
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A PRO 2058 HB2   /A LEU 2022 HB3    -0.354    2.354
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.357    3.057
    /A LEU 2022 HB3   /A PRO 2058 CB     -0.361    3.061
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A PRO 2058 CG    /A VAL 2057 CB     -0.369    3.769
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A LEU 2022 CB    /A PRO 2058 CD     -0.391    3.791
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A PRO 2058 HG2   /A VAL 2057 O      -0.393    2.813
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.400    3.100
    

  
130 contacts  

> name frozen Contacts sel

> select clear

> select Contacts

146 atoms, 74 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> select clear

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2022-2023

26 atoms, 25 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> select /A:2022-2023

26 atoms, 25 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2022-2023

26 atoms, 25 bonds, 2 pseudobonds, 2 residues, 2 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> show sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> select clear

> select /A:2025

19 atoms, 18 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> select /A:2025

19 atoms, 18 bonds, 2 pseudobonds, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

325 atoms, 323 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> close #1.1

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    130 contacts
         atom1             atom2        overlap  distance
    /A PRO 2058 HD2   /A VAL 2057 CB     1.082    1.618
    /A PRO 2058 HD2   /A VAL 2057 CG1    0.984    1.716
    /A VAL 2057 HB    /A PRO 2058 CD     0.618    2.082
    /A VAL 2057 CG1   /A PRO 2058 CD     0.603    2.797
    /A VAL 2057 HB    /A PRO 2058 HD2    0.482    1.518
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A PRO 2058 HD2   /A VAL 2057 HG13   0.201    1.799
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A PRO 2058 HD2   /A VAL 2057 HG12   0.194    1.806
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2022 HD21  /A PRO 2058 HG3    0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HB3   /A PRO 2058 HD3    0.025    1.975
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A VAL 2057 HB    /A PRO 2058 HD3    0.015    1.985
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A VAL 2057 HG13  /A PRO 2058 CD     -0.013    2.713
    /A VAL 2057 HG12  /A PRO 2058 CD     -0.013    2.713
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A LEU 2022 HB3   /A PRO 2058 CD     -0.097    2.797
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A PRO 2058 CG    /A VAL 2057 CG1    -0.112    3.512
    /A VAL 2057 CB    /A PRO 2058 HD3    -0.115    2.815
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2022 HD21  /A PRO 2058 CG     -0.135    2.835
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A LEU 2022 CB    /A PRO 2058 HD3    -0.144    2.844
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A PRO 2058 HD3   /A LEU 2022 O      -0.277    2.697
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A PRO 2058 CD    /A LEU 2022 O      -0.283    3.403
    /A PRO 2058 N     /A LEU 2022 O      -0.286    3.346
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 HG3   /A LEU 2022 CD2    -0.297    2.997
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A PRO 2058 HB2   /A LEU 2022 HB3    -0.354    2.354
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.357    3.057
    /A LEU 2022 HB3   /A PRO 2058 CB     -0.361    3.061
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A PRO 2058 CG    /A VAL 2057 CB     -0.369    3.769
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A LEU 2022 CB    /A PRO 2058 CD     -0.391    3.791
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A PRO 2058 HG2   /A VAL 2057 O      -0.393    2.813
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.400    3.100
    

  
130 contacts  

> name frozen Contacts sel

> select clear

> select Contacts

146 atoms, 74 bonds, 130 pseudobonds, 20 residues, 2 models selected  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    4 clashes
         atom1            atom2       overlap  distance
    /A PRO 2058 HD2  /A VAL 2057 CB    1.082    1.618
    /A VAL 2057 CG1  /A PRO 2058 HD2   0.984    1.716
    /A VAL 2057 HB   /A PRO 2058 CD    0.618    2.082
    /A PRO 2058 CD   /A VAL 2057 CG1   0.603    2.797
    

  
4 clashes  

> swapaa /A: 2058 leu

Using Dunbrack library  
/A PRO 2058: phi -137.9, psi 132.6 trans  
Applying LEU rotamer (chi angles: 177.6 65.4) to /A LEU 2058  

> close #1.1-2

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

320 atoms, 317 bonds, 20 residues, 1 model selected  

> select /A:2120-2121

25 atoms, 24 bonds, 2 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

320 atoms, 317 bonds, 20 residues, 1 model selected  

> select /A:2120-2121

25 atoms, 24 bonds, 2 residues, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

320 atoms, 317 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    112 contacts
         atom1             atom2        overlap  distance
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A VAL 2081 HG22  /A LEU 2058 CD1    0.269    2.611
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 H     /A LEU 2058 O      0.018    2.002
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A LEU 2058 CD1   /A ARG 2059 N      0.002    3.503
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2081 CG2   /A LEU 2058 CD1    -0.086    3.666
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A LEU 2058 CD1   /A ASN 2080 O      -0.095    3.395
    /A GLU 2021 HA    /A LEU 2058 O      -0.095    2.515
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A LEU 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A LEU 2058 CB    /A LEU 2022 HB3    -0.170    3.050
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A ARG 2059 H     /A LEU 2058 CD1    -0.240    3.120
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2022 N     /A LEU 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A ILE 2079 CG2   /A LEU 2058 CD1    -0.330    3.910
    /A LEU 2058 CG    /A ILE 2060 HG13   -0.330    3.210
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A LEU 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A LEU 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A ILE 2079 HG22  /A LEU 2058 CD1    -0.370    3.250
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A LEU 2058 CD2   /A ILE 2060 HD11   -0.375    3.255
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    

  
112 contacts  

> name frozen Contacts_leu sel

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> help help:user

> close #1.1-2

> swapaa /A: 2058 pro

Using Dunbrack library  
/A LEU 2058: phi -137.9, psi 132.6 trans  
Applying PRO rotamer (chi angles: -25.1 36.3) to /A PRO 2058  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    119 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 HB    /A PRO 2058 CD     0.804    2.076
    /A VAL 2057 CG1   /A PRO 2058 CD     0.792    2.788
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A VAL 2057 HG13  /A PRO 2058 CD     0.176    2.704
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 HG12  /A PRO 2058 CD     0.170    2.710
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A VAL 2057 CG1   /A PRO 2058 CG     0.082    3.498
    /A LEU 2022 HB3   /A PRO 2058 CD     0.073    2.807
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HD21  /A PRO 2058 CG     0.035    2.845
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A PRO 2058 CD    /A LEU 2022 O      -0.103    3.403
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A VAL 2057 CB    /A PRO 2058 CG     -0.176    3.756
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.185    3.065
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.189    3.069
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A LEU 2022 CB    /A PRO 2058 CD     -0.221    3.801
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.229    3.109
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A VAL 2057 HG13  /A PRO 2058 CG     -0.266    3.146
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A VAL 2057 HG12  /A PRO 2058 CG     -0.281    3.161
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 N     /A LEU 2022 O      -0.301    3.346
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A PRO 2058 CG    /A LEU 2022 CD2    -0.312    3.892
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    

  
119 contacts  

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    2 clashes
        atom1            atom2       overlap  distance
    /A VAL 2057 HB  /A PRO 2058 CD    0.804    2.076
    /A PRO 2058 CD  /A VAL 2057 CG1   0.792    2.788
    

  
2 clashes  

> ui windowfill toggle

> select clear

> ui windowfill toggle

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> select /A:2022

19 atoms, 18 bonds, 1 pseudobond, 1 residue, 2 models selected  

> show sel cartoons

[Repeated 1 time(s)]

> hide sel atoms

> ui windowfill toggle

[Repeated 5 time(s)]

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> ui windowfill toggle

[Repeated 1 time(s)]

> close #1.1

> ui windowfill toggle

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    119 contacts
         atom1             atom2        overlap  distance
    /A VAL 2057 HB    /A PRO 2058 CD     0.804    2.076
    /A VAL 2057 CG1   /A PRO 2058 CD     0.792    2.788
    /A ILE 2084 HG22  /A ALA 2082 O      0.435    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A ARG 2059 O     /A ASN 2080 H      0.258    1.762
    /A VAL 2057 CG2   /A GLY 2023 O      0.249    2.871
    /A LEU 2041 O     /A THR 2085 H      0.230    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.195    1.825
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A VAL 2057 HG13  /A PRO 2058 CD     0.176    2.704
    /A LEU 2020 H     /A ILE 2060 O      0.170    1.850
    /A VAL 2057 HG12  /A PRO 2058 CD     0.170    2.710
    /A VAL 2057 O     /A ALA 2082 H      0.168    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.156    2.264
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ARG 2059 H     /A ASN 2080 O      0.148    1.872
    /A ARG 2059 HA    /A LEU 2020 O      0.122    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.113    2.307
    /A LEU 2020 HD21  /A LEU 2020 C      0.098    2.512
    /A ILE 2084 HG13  /A ILE 2084 O      0.085    2.335
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A VAL 2057 CG1   /A PRO 2058 CG     0.082    3.498
    /A LEU 2022 HB3   /A PRO 2058 CD     0.073    2.807
    /A ILE 2084 CG2   /A ALA 2082 O      0.072    3.048
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A LEU 2022 HD21  /A PRO 2058 CG     0.035    2.845
    /A LEU 2022 H     /A PRO 2058 O      0.018    2.002
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A VAL 2057 H     /A LEU 2022 O      -0.039    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      -0.045    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      -0.046    2.466
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2041 H     /A THR 2085 O      -0.080    2.100
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 HA    /A PRO 2058 O      -0.095    2.515
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A PRO 2058 CD    /A LEU 2022 O      -0.103    3.403
    /A THR 2085 N     /A LEU 2041 O      -0.104    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.105    2.525
    /A PRO 2058 HA    /A ASN 2080 O      -0.106    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.106    2.526
    /A ASN 2080 N     /A ARG 2059 O      -0.107    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.117    2.537
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ARG 2059 CA    /A LEU 2020 O      -0.146    3.266
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ILE 2084 CA    /A LEU 2041 O      -0.164    3.284
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A VAL 2057 N     /A LEU 2022 O      -0.170    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.172    2.817
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A PRO 2083 C     /A ILE 2084 HG22   -0.176    2.786
    /A VAL 2057 CB    /A PRO 2058 CG     -0.176    3.756
    /A ASN 2024 OD1   /A ILE 2025 H      -0.178    2.198
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A PRO 2058 CB    /A LEU 2022 HB3    -0.185    3.065
    /A LEU 2022 HD21  /A PRO 2058 CD     -0.189    3.069
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A ILE 2060 O     /A LEU 2020 N      -0.212    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.214    2.859
    /A LEU 2022 CB    /A PRO 2058 CD     -0.221    3.801
    /A ARG 2059 N     /A ASN 2080 O      -0.227    2.872
    /A LEU 2022 HB3   /A PRO 2058 CG     -0.229    3.109
    /A ILE 2025 N     /A ASN 2024 OD1    -0.233    2.878
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2079 HA    /A ARG 2059 O      -0.253    2.673
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A VAL 2057 HG13  /A PRO 2058 CG     -0.266    3.146
    /A LEU 2022 N     /A PRO 2058 O      -0.268    2.913
    /A ILE 2025 H     /A ASN 2024 CG     -0.272    2.882
    /A ALA 2082 O     /A VAL 2081 CG1    -0.274    3.394
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A VAL 2057 HG12  /A PRO 2058 CG     -0.281    3.161
    /A GLU 2021 HG3   /A LEU 2020 C      -0.291    2.901
    /A PRO 2058 N     /A LEU 2022 O      -0.301    3.346
    /A ALA 2082 H     /A VAL 2057 C      -0.307    2.917
    /A LEU 2020 O     /A LEU 2020 HD21   -0.308    2.728
    /A PRO 2058 CG    /A LEU 2022 CD2    -0.312    3.892
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A VAL 2081 HG21  /A ASN 2080 C      -0.327    2.937
    /A VAL 2081 CA    /A VAL 2057 O      -0.336    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.337    3.457
    /A PRO 2058 O     /A GLU 2021 CA     -0.342    3.462
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ASN 2080 O     /A PRO 2058 CA     -0.344    3.464
    /A ILE 2060 H     /A LEU 2020 C      -0.344    2.954
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ASN 2080 H     /A ARG 2059 C      -0.361    2.971
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A THR 2085 H     /A LEU 2041 C      -0.373    2.983
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A GLU 2021 CG    /A LEU 2020 O      -0.393    3.513
    

  
119 contacts  

> ui windowfill toggle

[Repeated 3 time(s)]

> select clear

> ui windowfill toggle

> select /A:2078-2082

74 atoms, 73 bonds, 7 pseudobonds, 5 residues, 2 models selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 121 pseudobonds, 20 residues, 3 models selected  

> hide sel cartoons

> show sel atoms

> hide sel atoms

> show sel cartoons

[Repeated 1 time(s)]

> hide sel cartoons

[Repeated 1 time(s)]

> show sel cartoons

> ui mousemode right select

Drag select of 272 atoms, 262 residues, 253 bonds, 33 pseudobonds  

> hide sel atoms

> show sel cartoons

[Repeated 1 time(s)]

> select clear

> close #1.1-2

> select /A:2058

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

> color sel orange

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

319 atoms, 317 bonds, 20 residues, 1 model selected  
Drag select of 2 residues  

> ui mousemode right translate

> swapaa /A: 2058 leu

Using Dunbrack library  
/A PRO 2058: phi -137.9, psi 132.6 trans  
Applying LEU rotamer (chi angles: 177.6 65.4) to /A LEU 2058  

> select clear

> ui windowfill toggle

[Repeated 1 time(s)]

> save C:/Users/emirm/Desktop/contacts/Contacts.cxs

——— End of log from Tue Jul 29 15:17:34 2025 ———

> view name session-start

opened ChimeraX session  

> select /A:2058

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

> color sel red

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/ZoomedOut.tif width 1280 height 491
> supersample 3

> ui mousemode right select

Drag select of 262 residues  

> show sel surfaces

> transparency (#!1 & sel) 70

> select clear

> save C:/Users/emirm/Desktop/contacts/ZoomedOutSurface.tif width 1280 height
> 491 supersample 3

Drag select of fold_2025_02_26_14_57_hob_native_model_0.cif_A SES surface,
387556 of 3437070 triangles, 262 residues  

> hide sel surfaces

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to
fold_2025_02_26_14_57_hob_native_model_0.cif #1  
---  
notes | Termini for fold_2025_02_26_14_57_hob_native_model_0.cif (#1) chain A determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ASP 2300  
Chain-final residues that are not actual C termini:  
1819 hydrogen bonds  
10 hydrogens added  
  

> ui windowfill toggle

> select clear

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> select /A:2218

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:2218

24 atoms, 25 bonds, 1 residue, 1 model selected  

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> ui tool show Contacts

> contacts sel restrict both intraRes true ignoreHiddenModels true select true
> color #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    134 contacts
         atom1             atom2        overlap  distance
    /A ILE 2084 HG22  /A ALA 2082 O      0.495    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2059 O     /A ASN 2080 H      0.318    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.309    2.871
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A LEU 2041 O     /A THR 2085 H      0.290    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.255    1.825
    /A LEU 2020 H     /A ILE 2060 O      0.230    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.228    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.216    2.264
    /A ARG 2059 H     /A ASN 2080 O      0.208    1.872
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 HD21  /A LEU 2020 C      0.188    2.512
    /A ARG 2059 HA    /A LEU 2020 O      0.182    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.173    2.307
    /A LEU 2058 HD12  /A ASN 2080 O      0.171    2.309
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ILE 2084 HG13  /A ILE 2084 O      0.145    2.335
    /A ILE 2084 CG2   /A ALA 2082 O      0.132    3.048
    /A VAL 2081 HG22  /A LEU 2058 CD1    0.096    2.604
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A LEU 2022 H     /A LEU 2058 O      0.078    2.002
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2058 HA    /A LEU 2058 HD12   0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A VAL 2057 H     /A LEU 2022 O      0.021    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      0.015    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      0.014    2.466
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A LEU 2022 HB3   /A LEU 2058 HB2    -0.002    2.002
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A LEU 2041 H     /A THR 2085 O      -0.020    2.100
    /A LEU 2058 HG    /A ARG 2059 N      -0.021    2.646
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A GLU 2021 HA    /A LEU 2058 O      -0.035    2.515
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A THR 2085 N     /A LEU 2041 O      -0.044    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.045    2.525
    /A LEU 2058 HA    /A ASN 2080 O      -0.046    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.046    2.526
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ASN 2080 N     /A ARG 2059 O      -0.047    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.057    2.537
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2058 HD13  /A VAL 2081 HG22   -0.081    2.081
    /A PRO 2083 C     /A ILE 2084 HG22   -0.086    2.786
    /A ARG 2059 CA    /A LEU 2020 O      -0.086    3.266
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A ILE 2084 CA    /A LEU 2041 O      -0.104    3.284
    /A VAL 2057 N     /A LEU 2022 O      -0.110    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.112    2.817
    /A ASN 2024 OD1   /A ILE 2025 H      -0.118    2.198
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ILE 2060 O     /A LEU 2020 N      -0.152    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.154    2.859
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ARG 2059 N     /A ASN 2080 O      -0.167    2.872
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A ILE 2025 N     /A ASN 2024 OD1    -0.173    2.878
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A LEU 2058 CD1   /A ARG 2059 N      -0.181    3.506
    /A ILE 2025 H     /A ASN 2024 CG     -0.182    2.882
    /A ILE 2060 HD11  /A LEU 2058 HD21   -0.184    2.184
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A ILE 2079 HA    /A ARG 2059 O      -0.193    2.673
    /A GLU 2021 HG3   /A LEU 2020 C      -0.201    2.901
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A LEU 2022 N     /A LEU 2058 O      -0.208    2.913
    /A LEU 2058 CD1   /A ASN 2080 O      -0.211    3.391
    /A ALA 2082 O     /A VAL 2081 CG1    -0.214    3.394
    /A LEU 2058 HD12  /A ARG 2059 N      -0.216    2.841
    /A ALA 2082 H     /A VAL 2057 C      -0.217    2.917
    /A ARG 2059 H     /A LEU 2058 HD12   -0.233    2.233
    /A VAL 2081 HG21  /A ASN 2080 C      -0.237    2.937
    /A LEU 2020 O     /A LEU 2020 HD21   -0.248    2.728
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2060 H     /A LEU 2020 C      -0.254    2.954
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A VAL 2081 CG2   /A LEU 2058 CD1    -0.259    3.659
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2058 H     /A LEU 2022 O      -0.267    2.347
    /A ASN 2080 H     /A ARG 2059 C      -0.271    2.971
    /A VAL 2081 CA    /A VAL 2057 O      -0.276    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.277    3.457
    /A LEU 2058 HD21  /A ILE 2060 CD1    -0.280    2.980
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A LEU 2058 O     /A GLU 2021 CA     -0.282    3.462
    /A THR 2085 H     /A LEU 2041 C      -0.283    2.983
    /A ASN 2080 O     /A LEU 2058 CA     -0.284    3.464
    /A ILE 2079 HG22  /A LEU 2058 HD11   -0.300    2.300
    /A LEU 2058 HB2   /A LEU 2022 CB     -0.304    3.004
    /A LEU 2020 H     /A ILE 2060 C      -0.314    3.014
    /A ILE 2084 C     /A LEU 2041 O      -0.315    3.495
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A ILE 2060 HG13  /A ARG 2059 C      -0.333    3.033
    /A GLU 2021 CG    /A LEU 2020 O      -0.333    3.513
    /A ARG 2059 H     /A ASN 2080 C      -0.333    3.033
    /A ARG 2059 C     /A LEU 2020 O      -0.340    3.520
    /A LEU 2020 CD2   /A LEU 2020 O      -0.340    3.520
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A ILE 2084 HG22  /A ALA 2082 C      -0.348    3.048
    /A LEU 2058 CB    /A LEU 2022 HB3    -0.353    3.053
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ILE 2084 CB    /A LEU 2041 O      -0.357    3.537
    /A THR 2085 O     /A LEU 2041 N      -0.358    3.063
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A VAL 2057 CB    /A GLY 2023 O      -0.369    3.549
    /A LEU 2022 HG    /A ASN 2024 O      -0.372    2.852
    /A VAL 2057 CG2   /A GLY 2023 C      -0.375    3.775
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A LEU 2058 HD11  /A ILE 2079 CG2    -0.378    3.078
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A ILE 2079 CA    /A ARG 2059 O      -0.394    3.574
    /A ASN 2024 O     /A LEU 2022 CG     -0.396    3.576
    

  
134 contacts  

> ui windowfill toggle

[Repeated 1 time(s)]

> ui tool show Clashes

> clashes sel restrict both intraRes true ignoreHiddenModels true select true
> color #ff0000 reveal true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> ui windowfill toggle

[Repeated 1 time(s)]

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 134 pseudobonds, 20 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel color #00ff00 dashes 4 restrict both select true reveal true log
> true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    10 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N  /A ILE 2060 O  /A LEU 2020 H  2.857  1.850
    /A LEU 2022 N  /A LEU 2058 O  /A LEU 2022 H  2.913  2.002
    /A LEU 2041 N  /A THR 2085 O  /A LEU 2041 H  3.063  2.100
    /A VAL 2057 N  /A LEU 2022 O  /A VAL 2057 H  2.815  2.059
    /A LEU 2058 N  /A LEU 2022 O  /A LEU 2058 H  3.346  2.347
    /A ARG 2059 N  /A ASN 2080 O  /A ARG 2059 H  2.872  1.872
    /A ILE 2060 N  /A LEU 2020 O  /A ILE 2060 H  2.817  1.825
    /A ASN 2080 N  /A ARG 2059 O  /A ASN 2080 H  2.752  1.762
    /A ALA 2082 N  /A VAL 2057 O  /A ALA 2082 H  2.859  1.852
    /A THR 2085 N  /A LEU 2041 O  /A THR 2085 H  2.749  1.790
    

  
10 hydrogen bonds found  

> select clear

> hide #1.4 models

> hide #1.3 models

> select subtract #1.3

Nothing selected  

> hide #1.2 models

> show #1.2 models

> ui windowfill toggle

> ui mousemode right translate

> save C:/Users/emirm/Desktop/contacts/l2058_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.2 models

> show #1.3 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.3 models

> select subtract #1.3

Nothing selected  

> show #1.4 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_hb.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/session_L2058.cxs

——— End of log from Wed Jul 30 08:19:51 2025 ———

> view name session-start

opened ChimeraX session  

> close #1.2-4

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> ui tool show Contacts

> contacts sel saveFile C:/Users/emirm/Desktop/contacts/l2058_con_file
> restrict both intraRes true ignoreHiddenModels true select true color
> #ffffff dashes 4 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Detect intra-residue contacts: True
    Detect intra-molecule contacts: True
    
    134 contacts
         atom1             atom2        overlap  distance
    /A ILE 2084 HG22  /A ALA 2082 O      0.495    1.985
    /A ASN 2024 HA    /A VAL 2057 HG23   0.336    1.664
    /A ILE 2025 HG21  /A VAL 2057 HG12   0.327    1.673
    /A ARG 2059 O     /A ASN 2080 H      0.318    1.762
    /A GLY 2023 O     /A VAL 2057 CG2    0.309    2.871
    /A ARG 2026 HG3   /A LEU 2041 CD2    0.297    2.403
    /A LEU 2041 O     /A THR 2085 H      0.290    1.790
    /A LEU 2020 O     /A ILE 2060 H      0.255    1.825
    /A LEU 2020 H     /A ILE 2060 O      0.230    1.850
    /A VAL 2057 O     /A ALA 2082 H      0.228    1.852
    /A VAL 2057 HG13  /A VAL 2057 O      0.216    2.264
    /A ARG 2059 H     /A ASN 2080 O      0.208    1.872
    /A VAL 2057 HG12  /A ILE 2025 CG2    0.191    2.509
    /A LEU 2020 HD21  /A LEU 2020 C      0.188    2.512
    /A ARG 2059 HA    /A LEU 2020 O      0.182    2.298
    /A VAL 2081 HG11  /A ALA 2082 O      0.173    2.307
    /A LEU 2058 HD12  /A ASN 2080 O      0.171    2.309
    /A ILE 2084 HD11  /A ILE 2084 HG21   0.156    1.844
    /A ILE 2084 HG13  /A ILE 2084 O      0.145    2.335
    /A ILE 2084 CG2   /A ALA 2082 O      0.132    3.048
    /A VAL 2081 HG22  /A LEU 2058 CD1    0.096    2.604
    /A ILE 2025 HG21  /A VAL 2057 CG1    0.083    2.617
    /A LEU 2022 H     /A LEU 2058 O      0.078    2.002
    /A LEU 2041 CD2   /A ARG 2026 CG     0.064    3.336
    /A LEU 2058 HA    /A LEU 2058 HD12   0.053    1.947
    /A ARG 2059 HH11  /A ARG 2059 HD2    0.047    1.953
    /A VAL 2057 H     /A LEU 2022 O      0.021    2.059
    /A VAL 2057 HG23  /A GLY 2023 O      0.015    2.465
    /A VAL 2057 HG22  /A GLY 2023 O      0.014    2.466
    /A ARG 2026 HG3   /A LEU 2041 HD23   0.013    1.987
    /A ARG 2026 HG3   /A LEU 2041 HD22   0.013    1.987
    /A LEU 2022 HB3   /A LEU 2058 HB2    -0.002    2.002
    /A ARG 2059 HB3   /A ASN 2080 HB3    -0.009    2.009
    /A LEU 2041 H     /A THR 2085 O      -0.020    2.100
    /A LEU 2058 HG    /A ARG 2059 N      -0.021    2.646
    /A ASN 2024 HA    /A VAL 2057 CG2    -0.023    2.723
    /A ILE 2025 HB    /A LEU 2022 CD2    -0.023    2.723
    /A ILE 2079 HD13  /A ILE 2079 HG21   -0.029    2.029
    /A ILE 2025 HD13  /A ILE 2025 HG23   -0.032    2.032
    /A GLU 2021 HA    /A LEU 2058 O      -0.035    2.515
    /A ASN 2024 CA    /A VAL 2057 HG23   -0.037    2.737
    /A THR 2085 N     /A LEU 2041 O      -0.044    2.749
    /A VAL 2081 HA    /A VAL 2057 O      -0.045    2.525
    /A LEU 2058 HA    /A ASN 2080 O      -0.046    2.526
    /A ILE 2084 HA    /A LEU 2041 O      -0.046    2.526
    /A LEU 2022 HD22  /A ILE 2025 HB     -0.047    2.047
    /A ASN 2080 N     /A ARG 2059 O      -0.047    2.752
    /A ILE 2025 HG22  /A ILE 2025 O      -0.057    2.537
    /A ILE 2060 HD13  /A ILE 2060 HG21   -0.076    2.076
    /A LEU 2058 HD13  /A VAL 2081 HG22   -0.081    2.081
    /A PRO 2083 C     /A ILE 2084 HG22   -0.086    2.786
    /A ARG 2059 CA    /A LEU 2020 O      -0.086    3.266
    /A VAL 2057 HA    /A ALA 2082 CB     -0.091    2.791
    /A GLU 2021 N     /A LEU 2020 HD21   -0.097    2.722
    /A ILE 2060 HB    /A LEU 2020 HB3    -0.100    2.100
    /A ILE 2084 CA    /A LEU 2041 O      -0.104    3.284
    /A VAL 2057 N     /A LEU 2022 O      -0.110    2.815
    /A ILE 2060 N     /A LEU 2020 O      -0.112    2.817
    /A ASN 2024 OD1   /A ILE 2025 H      -0.118    2.198
    /A VAL 2057 CG1   /A ILE 2025 CG2    -0.121    3.521
    /A ALA 2082 HB1   /A PRO 2083 CD     -0.122    2.822
    /A LEU 2041 HD22  /A ARG 2026 CG     -0.139    2.839
    /A PRO 2083 HD2   /A ALA 2082 HA     -0.144    2.144
    /A ILE 2060 O     /A LEU 2020 N      -0.152    2.857
    /A ALA 2082 N     /A VAL 2057 O      -0.154    2.859
    /A ALA 2082 HB2   /A VAL 2057 HA     -0.156    2.156
    /A ILE 2079 HG23  /A VAL 2081 HG21   -0.159    2.159
    /A VAL 2081 HG11  /A ALA 2082 N      -0.163    2.788
    /A ARG 2059 N     /A ASN 2080 O      -0.167    2.872
    /A LEU 2041 HD23  /A ARG 2026 CG     -0.169    2.869
    /A ILE 2025 N     /A ASN 2024 OD1    -0.173    2.878
    /A LEU 2022 HD11  /A LEU 2022 HA     -0.175    2.175
    /A ILE 2079 HG23  /A VAL 2081 CG2    -0.180    2.880
    /A LEU 2058 CD1   /A ARG 2059 N      -0.181    3.506
    /A ILE 2025 H     /A ASN 2024 CG     -0.182    2.882
    /A ILE 2060 HD11  /A LEU 2058 HD21   -0.184    2.184
    /A ILE 2079 HG22  /A ILE 2060 HG12   -0.190    2.190
    /A ILE 2079 HA    /A ARG 2059 O      -0.193    2.673
    /A GLU 2021 HG3   /A LEU 2020 C      -0.201    2.901
    /A LEU 2041 HA    /A LEU 2041 HD22   -0.205    2.205
    /A LEU 2022 N     /A LEU 2058 O      -0.208    2.913
    /A LEU 2058 CD1   /A ASN 2080 O      -0.211    3.391
    /A ALA 2082 O     /A VAL 2081 CG1    -0.214    3.394
    /A LEU 2058 HD12  /A ARG 2059 N      -0.216    2.841
    /A ALA 2082 H     /A VAL 2057 C      -0.217    2.917
    /A ARG 2059 H     /A LEU 2058 HD12   -0.233    2.233
    /A VAL 2081 HG21  /A ASN 2080 C      -0.237    2.937
    /A LEU 2020 O     /A LEU 2020 HD21   -0.248    2.728
    /A PRO 2083 HD3   /A ALA 2082 HB1    -0.251    2.251
    /A ILE 2060 H     /A LEU 2020 C      -0.254    2.954
    /A GLU 2021 N     /A LEU 2020 CD2    -0.254    3.579
    /A ARG 2026 CD    /A LEU 2041 CD2    -0.255    3.655
    /A VAL 2081 CG2   /A LEU 2058 CD1    -0.259    3.659
    /A ARG 2059 HG3   /A GLU 2021 HG2    -0.264    2.264
    /A LEU 2058 H     /A LEU 2022 O      -0.267    2.347
    /A ASN 2080 H     /A ARG 2059 C      -0.271    2.971
    /A VAL 2081 CA    /A VAL 2057 O      -0.276    3.456
    /A PRO 2083 O     /A ILE 2084 CG2    -0.277    3.457
    /A LEU 2058 HD21  /A ILE 2060 CD1    -0.280    2.980
    /A ARG 2026 HH11  /A ARG 2026 HD3    -0.280    2.280
    /A LEU 2058 O     /A GLU 2021 CA     -0.282    3.462
    /A THR 2085 H     /A LEU 2041 C      -0.283    2.983
    /A ASN 2080 O     /A LEU 2058 CA     -0.284    3.464
    /A ILE 2079 HG22  /A LEU 2058 HD11   -0.300    2.300
    /A LEU 2058 HB2   /A LEU 2022 CB     -0.304    3.004
    /A LEU 2020 H     /A ILE 2060 C      -0.314    3.014
    /A ILE 2084 C     /A LEU 2041 O      -0.315    3.495
    /A ARG 2026 CD    /A LEU 2041 HD23   -0.316    3.016
    /A ILE 2060 HG13  /A ARG 2059 C      -0.333    3.033
    /A GLU 2021 CG    /A LEU 2020 O      -0.333    3.513
    /A ARG 2059 H     /A ASN 2080 C      -0.333    3.033
    /A ARG 2059 C     /A LEU 2020 O      -0.340    3.520
    /A LEU 2020 CD2   /A LEU 2020 O      -0.340    3.520
    /A ARG 2026 NE    /A LEU 2041 HD23   -0.343    2.968
    /A ILE 2025 HG13  /A ARG 2026 N      -0.346    2.971
    /A ILE 2084 HG22  /A ALA 2082 C      -0.348    3.048
    /A LEU 2058 CB    /A LEU 2022 HB3    -0.353    3.053
    /A VAL 2057 HG21  /A ALA 2042 CB     -0.353    3.053
    /A ILE 2084 CB    /A LEU 2041 O      -0.357    3.537
    /A THR 2085 O     /A LEU 2041 N      -0.358    3.063
    /A ASN 2080 HB3   /A ARG 2059 CB     -0.365    3.065
    /A ILE 2060 HG22  /A ILE 2079 HG13   -0.365    2.365
    /A LEU 2022 HD22  /A ILE 2025 CB     -0.366    3.066
    /A LEU 2022 HG    /A GLY 2023 N      -0.366    2.991
    /A ASN 2024 CA    /A VAL 2057 CG2    -0.369    3.769
    /A VAL 2057 CB    /A GLY 2023 O      -0.369    3.549
    /A LEU 2022 HG    /A ASN 2024 O      -0.372    2.852
    /A VAL 2057 CG2   /A GLY 2023 C      -0.375    3.775
    /A ARG 2059 HB3   /A ASN 2080 CB     -0.377    3.077
    /A LEU 2058 HD11  /A ILE 2079 CG2    -0.378    3.078
    /A ILE 2084 HG12  /A ILE 2084 H      -0.390    2.390
    /A THR 2085 HB    /A LEU 2041 HB2    -0.392    2.392
    /A ILE 2079 CA    /A ARG 2059 O      -0.394    3.574
    /A ASN 2024 O     /A LEU 2022 CG     -0.396    3.576
    

  
134 contacts  

> ui tool show Clashes

> clashes sel saveFile C:/Users/emirm/Desktop/contacts/l2058_cla_file restrict
> both intraRes true ignoreHiddenModels true select true color #ff0000 reveal
> true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: True
    Detect intra-molecule clashes: True
    
    0 clashes
    atom1  atom2  overlap  distance
    

  
No clashes  

> hide #1.3 models

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 134 pseudobonds, 20 residues, 2 models selected  

> ui tool show H-Bonds

> hbonds sel saveFile C:/Users/emirm/Desktop/contacts/l2058_hbond_file color
> #00ff00 dashes 4 restrict both select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 fold_2025_02_26_14_57_hob_native_model_0.cif
    
    10 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A LEU 2020 N  /A ILE 2060 O  /A LEU 2020 H  2.857  1.850
    /A LEU 2022 N  /A LEU 2058 O  /A LEU 2022 H  2.913  2.002
    /A LEU 2041 N  /A THR 2085 O  /A LEU 2041 H  3.063  2.100
    /A VAL 2057 N  /A LEU 2022 O  /A VAL 2057 H  2.815  2.059
    /A LEU 2058 N  /A LEU 2022 O  /A LEU 2058 H  3.346  2.347
    /A ARG 2059 N  /A ASN 2080 O  /A ARG 2059 H  2.872  1.872
    /A ILE 2060 N  /A LEU 2020 O  /A ILE 2060 H  2.817  1.825
    /A ASN 2080 N  /A ARG 2059 O  /A ASN 2080 H  2.752  1.762
    /A ALA 2082 N  /A VAL 2057 O  /A ALA 2082 H  2.859  1.852
    /A THR 2085 N  /A LEU 2041 O  /A THR 2085 H  2.749  1.790
    

  
10 hydrogen bonds found  

> hide #1.4 models

> select clear

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/session_L2058.cxs

[Repeated 1 time(s)]

> ui windowfill toggle

[Repeated 1 time(s)]

> save C:/Users/emirm/Desktop/contacts/l2058_con.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.2 models

> show #1.3 models

> select subtract #1.3

Nothing selected  

> hide #1.3 models

> show #1.3 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_cla.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.3 models

> show #1.4 models

> ui windowfill toggle

> save C:/Users/emirm/Desktop/contacts/l2058_hb.tif width 1280 height 491
> supersample 3

> ui windowfill toggle

> hide #1.4 models

> close #1.2-4

> select /A:2058

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

> select /A:2058

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

> color (#!1 & sel) orange red

> color (#!1 & sel) orange

> select /A:2081

16 atoms, 15 bonds, 1 residue, 1 model selected  

> select /A:2081

16 atoms, 15 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) red

> select /A:2147

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

> select /A:2147

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

> select /A:2020-2026,2041-2042,2057-2060,2079-2085

330 atoms, 327 bonds, 20 residues, 1 model selected  

> hide sel atoms

> show sel cartoons

> show sel atoms

[Repeated 1 time(s)]

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select add /A:2187

354 atoms, 350 bonds, 21 residues, 2 models selected  

> select add /A:2186

370 atoms, 365 bonds, 22 residues, 2 models selected  

> select add /A:2185

384 atoms, 379 bonds, 23 residues, 2 models selected  

> select add /A:2184

400 atoms, 394 bonds, 24 residues, 2 models selected  

> select subtract /A:2184

384 atoms, 379 bonds, 23 residues, 2 models selected  

> select add /A:2184

400 atoms, 394 bonds, 24 residues, 2 models selected  

> select add /A:2183

415 atoms, 408 bonds, 25 residues, 2 models selected  

> select add /A:2181

434 atoms, 426 bonds, 26 residues, 2 models selected  

> select add /A:2182

448 atoms, 440 bonds, 27 residues, 2 models selected  

> show sel atoms

> hide sel atoms

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select subtract /A:2020

429 atoms, 421 bonds, 26 residues, 2 models selected  

> select subtract /A:2021

414 atoms, 406 bonds, 25 residues, 2 models selected  

> select subtract /A:2022

395 atoms, 387 bonds, 24 residues, 2 models selected  

> select subtract /A:2023

388 atoms, 380 bonds, 23 residues, 2 models selected  

> select subtract /A:2024

374 atoms, 366 bonds, 22 residues, 2 models selected  

> select subtract /A:2025

355 atoms, 347 bonds, 21 residues, 2 models selected  

> select subtract /A:2042

345 atoms, 337 bonds, 20 residues, 2 models selected  

> select subtract /A:2041

326 atoms, 319 bonds, 19 residues, 2 models selected  

> select subtract /A:2026

302 atoms, 296 bonds, 18 residues, 2 models selected  

> select add /A:2041

321 atoms, 314 bonds, 19 residues, 2 models selected  

> select add /A:2042

331 atoms, 323 bonds, 20 residues, 2 models selected  

> select add /A:2040

350 atoms, 341 bonds, 21 residues, 2 models selected  

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> select /A:2237

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

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> select /A:2237-2238

28 atoms, 27 bonds, 2 residues, 1 model selected  

> select /A:2040-2042,2057-2060,2079-2085,2181-2187

350 atoms, 349 bonds, 21 residues, 1 model selected  

> save C:/Users/emirm/Desktop/contacts/session_V2081.cxs

——— End of log from Wed Jul 30 09:34:05 2025 ———

> view name session-start

opened ChimeraX session  




OpenGL version: 3.3.0 Core Profile Context 24.3.1.240216
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.8.1, Qt 6.8.2
Qt runtime version: 6.8.2
Qt platform: windows

Manufacturer: ASUSTeK COMPUTER INC.
Model: Zenbook UX425QA_UM425QA
OS: Microsoft Windows 11 Pro (Build 26100)
Memory: 16,536,301,568
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 9 5900HX with Radeon Graphics        
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.2.0
    babel: 2.17.0
    beautifulsoup4: 4.13.3
    blockdiag: 3.0.0
    blosc2: 3.2.0
    build: 1.2.2.post1
    certifi: 2025.1.31
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.1
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.19.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.1.1
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.5
    ChimeraX-AtomicLibrary: 14.1.13
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    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-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.10.dev202503131841
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.5.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    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-maskChains: 1.4
    ChimeraX-MatchMaker: 2.1.7
    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: 2.15
    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: 1.14.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.7
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-ProfileGrids: 1.0.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.3
    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: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17
    ChimeraX-Shape: 1.1
    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: 1.19.1
    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: 2.5.2
    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-UI: 1.44
    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
    comtypes: 1.4.5
    contourpy: 1.3.1
    coverage: 7.6.12
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.12
    debugpy: 1.8.13
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.17.0
    fonttools: 4.56.0
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h5py: 3.13.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.0.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.6
    joblib: 1.4.2
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.8
    line_profiler: 4.2.0
    llvmlite: 0.44.0
    lxml: 5.3.1
    lz4: 4.4.3
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.1.0
    narwhals: 1.30.0
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numba: 0.61.0
    numexpr: 2.10.2
    numpy: 2.1.3
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.0.1
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    plotly: 6.0.0
    pluggy: 1.5.0
    prompt_toolkit: 3.0.50
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.32
    Pygments: 2.18.0
    pyKVFinder: 0.7.3
    pynmrstar: 3.3.5
    pynndescent: 0.5.13
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.1
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.8.1
    PyQt6-Qt6: 6.8.2
    PyQt6-WebEngine-commercial: 6.8.0
    PyQt6-WebEngine-Qt6: 6.8.2
    PyQt6_sip: 13.10.0
    pytest: 8.3.5
    pytest-cov: 6.0.0
    python-dateutil: 2.9.0.post0
    pytz: 2025.1
    pywin32: 306
    pyzmq: 26.3.0
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.3
    roman-numerals-py: 3.1.0
    scikit-learn: 1.6.1
    scipy: 1.14.0
    setuptools: 75.8.2
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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: 0.7.1
    tables: 3.10.2
    tcia_utils: 1.5.1
    threadpoolctl: 3.5.0
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    toml: 0.10.2
    tornado: 6.4.2
    tqdm: 4.67.1
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2025.1
    umap-learn: 0.5.7
    urllib3: 2.3.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.13
    WMI: 1.5.1

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