Crash starting ISOLDE

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-28-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
tried tttttttttttttttttttttttttto start isolde but it crashed 
Fatal Python error: Segmentation fault

Current thread 0x0000707a041ff640 (most recent call first):
  File "/home/pinkie/.local/share/ChimeraX/1.5/site-packages/chimerax/isolde/openmm/forcefields.py", line 66 in _background_load_ff
  File "/usr/lib/ucsf-chimerax/lib/python3.9/concurrent/futures/thread.py", line 58 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/concurrent/futures/thread.py", line 83 in _worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707b315f5640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 1297 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a2e7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a2effd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a2f7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a2ffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4cff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4d7fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4dffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4e7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4effd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4f7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a4ffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6cff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6d7fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6dffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6e7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6effd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6f7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a6ffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8cff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8d7fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8dffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8e7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8effd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8f7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707a8ffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aacff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aad7fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aadffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aae7fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aaeffd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aaf7fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707aaffff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707ad4ff9640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707ad57fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707ad5ffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x0000707b7709db80 (most recent call first):
  File "", line 142 in _path_stat
  File "", line 148 in _path_is_mode_type
  File "", line 163 in _path_isdir
  File "", line 1608 in path_hook_for_FileFinder
  File "", line 1340 in _path_hooks
  File "", line 1364 in _path_importer_cache
  File "", line 1392 in _get_spec
  File "", line 1423 in find_spec
  File "", line 925 in _find_spec
  File "", line 982 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/home/pinkie/.local/share/ChimeraX/1.5/site-packages/chimerax/isolde/validation/ramaplot/tool.py", line 6 in 
  File "", line 228 in _call_with_frames_removed
  File "", line 850 in exec_module
  File "", line 680 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/home/pinkie/.local/share/ChimeraX/1.5/site-packages/chimerax/isolde/validation/ramaplot/__init__.py", line 2 in 
  File "", line 228 in _call_with_frames_removed
  File "", line 850 in exec_module
  File "", line 680 in _load_unlocked
  File "", line 986 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "", line 228 in _call_with_frames_removed
  File "", line 972 in _find_and_load_unlocked
  File "", line 1007 in _find_and_load
  File "/home/pinkie/.local/share/ChimeraX/1.5/site-packages/chimerax/isolde/isolde.py", line 720 in register_next_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 134 in invoke
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 217 in _activate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 186 in activate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/triggerset.py", line 354 in activate_trigger
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 54 in draw_new_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/updateloop.py", line 139 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 283 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 884 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/__main__.py", line 1035 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/usr/lib/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open /home/pinkie/Documents/Charlotte/2024_06/done-brd4-n8.cxs

Opened cryosparc_P9_J412_002_volume_map_sharp.mrc z flip as #17, grid size
144,144,144, pixel 2.47, shown at level 0.153, step 1, values float32  
Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #20, grid size
420,420,420, pixel 0.825, shown at level 0.0707, step 1, values float32  
Opened cryosparc_P14_J581_003_volume_map_sharp.mrc z flip as #22, grid size
128,128,128, pixel 3.38, shown at level 0.405, step 1, values float32  
Opened cryosparc_P9_J659_007_volume_map_sharp.mrc as #1.1, grid size
480,480,480, pixel 0.825, shown at level 0.264, step 1, values float32  
Opened cryosparc_P9_J659_007_volume_map.mrc as #1.2, grid size 480,480,480,
pixel 0.825, shown at level 0.0962, step 1, values float32  
Log from Wed Jun 26 10:54:46 2024UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_30_v2_chimerasession.cxs

Opened cryosparc_P9_J412_002_volume_map_sharp.mrc z flip as #17, grid size
144,144,144, pixel 2.47, shown at level 0.153, step 1, values float32  
Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #20, grid size
420,420,420, pixel 0.825, shown at level 0.0707, step 1, values float32  
Opened cryosparc_P14_J581_003_volume_map_sharp.mrc z flip as #22, grid size
128,128,128, pixel 3.38, shown at level 0.255, step 1, values float32  
Log from Tue Jan 30 11:29:44 2024UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J710_006_volume_map_sharp.mrc

Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32  

> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v4.pdb

Chain information for fullmodel-v4.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
R | No description available  
  

> volume #1 level 0.204

> show cartoons

> hide atoms

> volume #1 level 0.1434

> transparency 50

> surface dust #1 size 14.8

> select #2/R

1432 atoms, 1452 bonds, 92 residues, 1 model selected  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for fullmodel-v4.pdb  
---  
Chain | Description  
2.2/A | No description available  
2.2/B | No description available  
2.2/C | No description available  
2.2/D | No description available  
2.2/E | No description available  
2.2/R | No description available  
  

> select clear

> clipper associate #1 toModel #2

Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #2.1.1.1, grid size
256,256,256, pixel 1.48, shown at step 1, values float32  

> volume #2.1.1.1 level 0.0992

> select #2/R

1432 atoms, 1452 bonds, 92 residues, 1 model selected  

> select clear

> select #2/R:38-108

1106 atoms, 1122 bonds, 71 residues, 1 model selected  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> isolde sim resume

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> hide #!2.1 models

> show #!2.1 models

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J710_006_volume_map_sharp.mrc

Opened cryosparc_P7_J710_006_volume_map_sharp.mrc as #1, grid size
256,256,256, pixel 1.48, shown at level 0.0524, step 1, values float32  

> volume #1 level 0.1585

> save /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb

> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v4.pdb

Chain information for fullmodel-v4.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
R | No description available  
  

> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb

Chain information for fullmodel-v5.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
R | No description available  
  

> hide #!2 models

> hide #!2.1 models

> hide #!2.2 models

> hide #2.3 models

> hide #3-4 atoms

> show #3-4 cartoons

> transparency #1.1 50

> hide #3 models

> hide #4 models

> show #4 models

> hide #4 models

> show #4 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> hide #4 models

> show #4 models

> open 5t35

5t35 title:  
The PROTAC MZ1 in complex with the second bromodomain of Brd4 and
pVHL:ElonginC:ElonginB [more info...]  
  
Chain information for 5t35 #5  
---  
Chain | Description | UniProt  
A E | Bromodomain-containing protein 4 | BRD4_HUMAN  
B F | Transcription elongation factor B polypeptide 2 | ELOB_HUMAN  
C G | Transcription elongation factor B polypeptide 1 | ELOC_HUMAN  
D H | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
  
Non-standard residues in 5t35 #5  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
  
5t35 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> select #5/E

910 atoms, 918 bonds, 126 residues, 1 model selected  

> delete sel

> select #5/G

693 atoms, 703 bonds, 1 pseudobond, 92 residues, 2 models selected  

> delete sel

> select #5/F

811 atoms, 826 bonds, 105 residues, 1 model selected  

> delete sel

> select #5/H

1265 atoms, 1294 bonds, 156 residues, 1 model selected  

> delete sel

> ui tool show Matchmaker

> matchmaker #!5 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain B (#4) with 5t35, chain D (#5), sequence
alignment score = 792.2  
RMSD between 149 pruned atom pairs is 0.891 angstroms; (across all 149 pairs:
0.891)  
  

> matchmaker #!5 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain B (#4) with 5t35, chain D (#5), sequence
alignment score = 792.2  
RMSD between 149 pruned atom pairs is 0.891 angstroms; (across all 149 pairs:
0.891)  
  

> hide #4#!5 atoms

> select ::name="759"

69 atoms, 75 bonds, 1 residue, 1 model selected  

> show sel atoms

> color sel yellow

> color sel byhetero

> select clear

> select #4/A

1835 atoms, 1858 bonds, 114 residues, 1 model selected  

> color sel #5b42cdff

> select #4/B

2615 atoms, 2648 bonds, 160 residues, 1 model selected  

> color sel #bfbfbfff

> color sel #fafafaff

[Repeated 1 time(s)]

> color sel forest green

> select #4/C

1647 atoms, 1663 bonds, 104 residues, 1 model selected  

> color sel #bdbf40ff

> color sel #bdbf3aff

> color sel #ccce3fff

[Repeated 3 time(s)]

> select #4/D

1522 atoms, 1539 bonds, 97 residues, 1 model selected  

> color sel #54bf40ff

> color sel #9abf93ff

> color sel #b0daa8ff

[Repeated 3 time(s)]

> select #4/E

10756 atoms, 10867 bonds, 658 residues, 1 model selected  

> color sel #40a8bfff

> color sel #4daabfff

> color sel #4293a5ff

[Repeated 3 time(s)]

> select #4/R

1432 atoms, 1452 bonds, 92 residues, 1 model selected  

> color sel #5ebf40ff

> color sel #5abf3aff

> color sel #60cb3eff

[Repeated 3 time(s)]

> select clear

> set bgColor white

> set bgColor #ffffff00

> lighting soft

> show #!1 models

> hide #!1 models

> save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
> height 803 supersample 3 transparentBackground true

> graphics silhouettes true

> save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
> height 803 supersample 3

> save /home/pinkie/Documents/Charlotte/2024_01_28/view-back.png width 1269
> height 803 supersample 3 transparentBackground true

> open 5n4w

5n4w title:  
Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex [more
info...]  
  
Chain information for 5n4w #6  
---  
Chain | Description | UniProt  
A | Cullin-2 | CUL2_HUMAN  
B | Elongin-B | ELOB_HUMAN  
C | Elongin-C | ELOC_HUMAN  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN  
V | Von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
  
Non-standard residues in 5n4w #6  
---  
ZN — zinc ion  
  

> ui tool show Matchmaker

> matchmaker #!6 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain E (#4) with 5n4w, chain A (#6), sequence
alignment score = 3288.4  
RMSD between 377 pruned atom pairs is 1.063 angstroms; (across all 587 pairs:
3.224)  
  

> matchmaker #!6 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain E (#4) with 5n4w, chain A (#6), sequence
alignment score = 3288.4  
RMSD between 377 pruned atom pairs is 1.063 angstroms; (across all 587 pairs:
3.224)  
  

> select add #6

7719 atoms, 7841 bonds, 29 pseudobonds, 970 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #!6 models

> show #3 models

> hide #3 models

> show #3 models

> close #3

> close #2

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> save /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_28__npn-
> crosslinked-structure__final.cxs includeMaps true

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map.mrc
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map_sharp.mrc
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J647_006_volume_map_sharp.mrc
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J659_007_volume_map.mrc

Opened cryosparc_P9_J635_008_volume_map.mrc as #2.1, grid size 480,480,480,
pixel 0.825, shown at level 0.00758, step 2, values float32  
Opened cryosparc_P9_J635_008_volume_map_sharp.mrc as #2.2, grid size
480,480,480, pixel 0.825, shown at level 0.0194, step 2, values float32  
Opened cryosparc_P9_J647_006_volume_map_sharp.mrc as #2.3, grid size
480,480,480, pixel 0.825, shown at level 0.0203, step 2, values float32  
Opened cryosparc_P9_J659_007_volume_map.mrc as #2.4, grid size 480,480,480,
pixel 0.825, shown at level 0.00707, step 2, values float32  

> volume #2.4 level 0.04195

> volume #2.3 level 0.07573

> volume #2.2 level 0.06618

> volume #2.1 level 0.03781

> surface dust #2.1 size 8.25

> surface dust #2.2 size 8.25

> surface dust #2.3 size 8.25

> surface dust #2.4 size 8.25

> volume flip #2.2

Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #3, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

> close #2.2

> select add #2.3

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2.3,0.98461,-0.13581,0.11,9.4722,-0.13019,-0.98986,-0.056778,424.6,0.1166,0.041583,-0.99231,332.63

> volume flip #2.3

Opened cryosparc_P9_J647_006_volume_map_sharp.mrc z flip as #7, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

> close #2.3

> select add #7

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.94093,0.053579,0.33434,-66.51,-0.17685,0.91978,0.35032,-21.349,-0.28875,-0.38875,0.87493,94.987

> view matrix models
> #7,0.9958,-0.06531,0.064213,3.5056,-0.016537,-0.81777,-0.5753,480.25,0.090084,0.57182,-0.81542,197.79

> view matrix models
> #7,-0.94582,-0.18918,-0.2639,470.69,0.14941,-0.97515,0.16355,320.99,-0.28828,0.11526,0.95058,-18.388

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.94582,-0.18918,-0.2639,476.46,0.14941,-0.97515,0.16355,320.85,-0.28828,0.11526,0.95058,43.172

> ui mousemode right "translate selected models"

> view matrix models
> #7,-0.94582,-0.18918,-0.2639,476.75,0.14941,-0.97515,0.16355,319.58,-0.28828,0.11526,0.95058,47.965

> fitmap #3 inMap #1

Fit map cryosparc_P9_J635_008_volume_map_sharp.mrc z flip in map
cryosparc_P7_J710_006_volume_map_sharp.mrc using 260097 points  
correlation = 0.7239, correlation about mean = 0.415, overlap = 7246  
steps = 108, shift = 10.4, angle = 7.23 degrees  
  
Position of cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#3) relative to
cryosparc_P7_J710_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99741254 0.03385855 0.06341789 -25.04544197  
-0.04024254 0.99394367 0.10225709 -19.05719275  
-0.05957154 -0.10454460 0.99273444 35.75883607  
Axis -0.82141607 0.48851388 -0.29432945  
Axis point 0.00000000 329.56848775 209.41103196  
Rotation angle (degrees) 7.23164693  
Shift along axis 0.73814676  
  

> fitmap #7 inMap #1

Fit map cryosparc_P9_J647_006_volume_map_sharp.mrc z flip in map
cryosparc_P7_J710_006_volume_map_sharp.mrc using 215940 points  
correlation = 0.7306, correlation about mean = 0.3854, overlap = 6936  
steps = 208, shift = 9.46, angle = 21.8 degrees  
  
Position of cryosparc_P9_J647_006_volume_map_sharp.mrc z flip (#7) relative to
cryosparc_P7_J710_006_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
-0.99893793 -0.00322217 0.04596451 381.28217401  
0.00554917 -0.99870419 0.05058868 376.53393934  
0.04574195 0.05079001 0.99766132 -20.33401849  
Axis 0.02293995 0.02535860 0.99941518  
Axis point 190.46107391 188.94352871 0.00000000  
Rotation angle (degrees) 179.74857166  
Shift along axis -2.02715908  
  

> hide #!5 models

> hide #4 models

> show #4 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!3 models

> select clear

> surface dust #3 size 8.25

> surface dust #7 size 8.25

> hide #!3 models

> show #!3 models

> volume #7 level 0.07801

> volume #3 level 0.05626

> select clear

> transparency #3.1 50

> volume #!3 style surface

[Repeated 1 time(s)]

> open 6ttu

6ttu title:  
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]  
  
Chain information for 6ttu #8  
---  
Chain | Description | UniProt  
C | Cullin-1 | CUL1_HUMAN  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN  
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |  
N | NEDD8 | NEDD8_HUMAN  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN  
S | S-phase kinase-associated protein 1 | SKP1_HUMAN  
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN  
U | Polyubiquitin-C | UBC_HUMAN  
  
Non-standard residues in 6ttu #8  
---  
ZN — zinc ion  
  

> select add #8

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #8/I

58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected  

> delete sel

> select #8/T

3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected  

> delete sel

> select #8/S

891 atoms, 903 bonds, 3 pseudobonds, 123 residues, 2 models selected  

> delete sel

> ui tool show Matchmaker

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> hide #!8 models

> hide #!3 models

> show #!8 models

> matchmaker #8/C to #4/E pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1628.1  
RMSD between 309 pruned atom pairs is 1.282 angstroms; (across all 619 pairs:
4.270)  
  

> matchmaker #8/C to #4/E pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1628.1  
RMSD between 309 pruned atom pairs is 1.282 angstroms; (across all 619 pairs:
4.270)  
  

> select #8/C:15-354

2540 atoms, 2582 bonds, 3 pseudobonds, 305 residues, 2 models selected  

> delete sel

> select #8/C:703-776

582 atoms, 587 bonds, 1 pseudobond, 70 residues, 2 models selected  

> delete sel

> ui tool show Matchmaker

> matchmaker #8/C to #4/E pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1250.8  
RMSD between 194 pruned atom pairs is 1.196 angstroms; (across all 316 pairs:
2.691)  
  

> matchmaker #8/C to #4/E pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain E (#4) with 6ttu, chain C (#8), sequence
alignment score = 1250.8  
RMSD between 194 pruned atom pairs is 1.196 angstroms; (across all 316 pairs:
2.691)  
  

> ui tool show Matchmaker

> matchmaker #8/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 466.8  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  

> matchmaker #8/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 466.8  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  

> ui tool show Matchmaker

> select #8/C

2606 atoms, 2650 bonds, 1 pseudobond, 326 residues, 2 models selected  

> delete sel

> close #6

> show #!7 models

> hide #!7 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> hide #!1 models

> show #!7 models

> hide #!7 models

> show #!5 models

> hide #!5 models

> select add #4

19807 atoms, 20027 bonds, 1225 residues, 1 model selected  

> select add #8

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected  

> combine sel

Remapping chain ID 'D' in 6ttu #8 to 'F'  
Remapping chain ID 'R' in 6ttu #8 to 'S'  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 21 residues in model #6 to IUPAC-IUB
standards.  

> select clear

> clipper associate #3 toModel #6

Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #6.1.1.1, grid
size 480,480,480, pixel 0.825, shown at step 1, values float32  

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J635_008_volume_map_sharp.mrc

Opened cryosparc_P9_J635_008_volume_map_sharp.mrc as #3, grid size
480,480,480, pixel 0.825, shown at level 0.0194, step 2, values float32  

> volume #3 level 0.09358

> volume flip #3

Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #9, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 2 maps.  

> hide #!6.2 models

> show #!6.2 models

> select add #6.2

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 8 models selected  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 3 atomic models, 2 maps.  

> select add #6.2

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 8 models selected  

> select add #6

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 15 models selected  

> close #6

> hide #!9 models

> select add #4

19807 atoms, 20027 bonds, 1225 residues, 1 model selected  

> select add #8

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected  

> combine sel

Remapping chain ID 'D' in 6ttu #8 to 'F'  
Remapping chain ID 'R' in 6ttu #8 to 'S'  

> hide #4 models

> select subtract #4

2984 atoms, 3047 bonds, 13 pseudobonds, 380 residues, 3 models selected  

> hide #!8 models

> select subtract #8

Nothing selected  

> select add #6

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 3 models selected  

> show #!9 models

> fitmap #6 inMap #9

Fit molecule combination (#6) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) using 22791 atoms  
average map value = 0.0972, steps = 156  
shifted from previous position = 11.3  
rotated from previous position = 6.89 degrees  
atoms outside contour = 12780, contour level = 0.093576  
  
Position of combination (#6) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) coordinates:  
Matrix rotation and translation  
0.99761374 -0.02131244 -0.06567050 24.02263064  
0.01475408 0.99499981 -0.09878107 25.91855777  
0.06744740 0.09757645 0.99293992 -32.41202814  
Axis 0.81831656 -0.55476655 0.15030663  
Axis point 0.00000000 350.66445652 246.92285576  
Rotation angle (degrees) 6.89074657  
Shift along axis 0.40762520  
  

> select clear

> hide #!6 models

> show #!6 models

> ui tool show Matchmaker

> matchmaker #6/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with combination, chain R (#6),
sequence alignment score = 927  
RMSD between 89 pruned atom pairs is 0.000 angstroms; (across all 89 pairs:
0.000)  
  

> matchmaker #6/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with combination, chain R (#6),
sequence alignment score = 927  
RMSD between 89 pruned atom pairs is 0.000 angstroms; (across all 89 pairs:
0.000)  
  

> hide #!6 models

> show #!6 models

> hide #!6 models

> show #!6 models

> hide #!9 models

> show #!9 models

> hide #!9 models

> ui tool show Matchmaker

> close #6

> show #4 models

> show #!8 models

> combine sel

No structures specified  

> select add #4

19807 atoms, 20027 bonds, 1225 residues, 1 model selected  

> select add #8

22791 atoms, 23074 bonds, 13 pseudobonds, 1605 residues, 4 models selected  

> select subtract #8

19807 atoms, 20027 bonds, 1225 residues, 1 model selected  

> hide #!8 models

> hide #4 models

> show #4 models

> show #!9 models

> select add #9

19807 atoms, 20027 bonds, 1225 residues, 3 models selected  

> fitmap #4 inMap #9

Fit molecule fullmodel-v5.pdb (#4) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) using 19807 atoms  
average map value = 0.1121, steps = 152  
shifted from previous position = 10.8  
rotated from previous position = 6.89 degrees  
atoms outside contour = 9792, contour level = 0.093576  
  
Position of fullmodel-v5.pdb (#4) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#9) coordinates:  
Matrix rotation and translation  
0.99762593 -0.02091198 -0.06561397 23.93517264  
0.01436000 0.99500528 -0.09878407 25.98670381  
0.06735202 0.09760733 0.99294336 -32.41050705  
Axis 0.81905399 -0.55453714 0.14710244  
Axis point 0.00000000 350.60177499 247.72967437  
Rotation angle (degrees) 6.88570607  
Shift along axis 0.42594157  
  

> select clear

> hide #!9 models

> show #!8 models

> ui tool show Matchmaker

> matchmaker #8/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 499.8  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> matchmaker #8/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 499.8  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  

> matchmaker #8/R to #4/R pairing ss

Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 499.8  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  

> ui tool show Matchmaker

[Repeated 1 time(s)]Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> matchmaker #!8 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 476.4  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  

> matchmaker #!8 to #4

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fullmodel-v5.pdb, chain R (#4) with 6ttu, chain R (#8), sequence
alignment score = 476.4  
RMSD between 39 pruned atom pairs is 1.214 angstroms; (across all 78 pairs:
14.356)  
  

> select add #8

2984 atoms, 3047 bonds, 13 pseudobonds, 380 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.5203,0.56446,-0.64084,135.43,0.36003,-0.82545,-0.43475,422.57,-0.77438,-0.0045259,-0.6327,409.12

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.5203,0.56446,-0.64084,121.21,0.36003,-0.82545,-0.43475,360.91,-0.77438,-0.0045259,-0.6327,411.66

> view matrix models
> #8,0.5203,0.56446,-0.64084,67.915,0.36003,-0.82545,-0.43475,357.48,-0.77438,-0.0045259,-0.6327,425.56

> view matrix models
> #8,0.5203,0.56446,-0.64084,83.916,0.36003,-0.82545,-0.43475,369.99,-0.77438,-0.0045259,-0.6327,452.45

> view matrix models
> #8,0.5203,0.56446,-0.64084,75.872,0.36003,-0.82545,-0.43475,367.76,-0.77438,-0.0045259,-0.6327,456.02

> view matrix models
> #8,0.5203,0.56446,-0.64084,74.881,0.36003,-0.82545,-0.43475,370.35,-0.77438,-0.0045259,-0.6327,456.29

> view matrix models
> #8,0.5203,0.56446,-0.64084,75.862,0.36003,-0.82545,-0.43475,369.49,-0.77438,-0.0045259,-0.6327,457.55

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #8,0.2363,0.60838,-0.75765,130.06,0.41768,-0.76762,-0.48612,357.73,-0.87733,-0.20159,-0.43549,479.62

> ui mousemode right "translate selected models"

> view matrix models
> #8,0.2363,0.60838,-0.75765,133.58,0.41768,-0.76762,-0.48612,354.6,-0.87733,-0.20159,-0.43549,486.99

> view matrix models
> #8,0.2363,0.60838,-0.75765,133.86,0.41768,-0.76762,-0.48612,354.1,-0.87733,-0.20159,-0.43549,487.38

> select clear

> select #8/R:19-39

184 atoms, 190 bonds, 21 residues, 1 model selected  

> delete sel

Undo failed, probably because structures have been modified.  

> hide #!8 models

> show #!8 models

> show #!9 models

> hide #!8 models

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
Chain information for fullmodel-v5.pdb  
---  
Chain | Description  
4.2/A | No description available  
4.2/B | No description available  
4.2/C | No description available  
4.2/D | No description available  
4.2/E | No description available  
4.2/R | No description available  
  

> clipper associate #9 toModel #4

Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #4.1.1.1, grid
size 480,480,480, pixel 0.825, shown at step 1, values float32  

> view matrix models #4.2,1,0,0,0.56548,0,1,0,-4.8388,0,0,1,-5.2016

> show #!3 models

> hide #!3 models

> isolde sim start sel

ISOLDE: started sim  

> isolde sim pause

> hide #!4 models

> show #!4 models

> hide #!4.1 models

> show #!4.1 models

> volume #!4.1.1.1 style surface

> fitmap #4.2 inMap #4.1.1.1

Fit molecule fullmodel-v5.pdb (#4.2) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#4.1.1.1) using 19807 atoms  
average map value = 0.1316, steps = 140  
shifted from previous position = 7.11  
rotated from previous position = 0.0441 degrees  
atoms outside contour = 15522, contour level = 0.19368  
  
Position of fullmodel-v5.pdb (#4.2) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#4.1.1.1) coordinates:  
Matrix rotation and translation  
0.99999973 -0.00058113 0.00045808 0.02446487  
0.00058103 0.99999981 0.00021172 -0.18611887  
-0.00045820 -0.00021146 0.99999987 0.13541812  
Axis -0.27492671 0.59527919 0.75502185  
Axis point 304.68612802 34.72877780 0.00000000  
Rotation angle (degrees) 0.04409607  
Shift along axis -0.01527510  
  

> isolde sim resume

> isolde sim pause

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 39 residues in model #4.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start sel

ISOLDE: started sim  

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 50 residues in model #4.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /home/pinkie/Documents/Charlotte/2024_01_28/fulmodel-v6-crosslinked.pdb
> models #4

> hide #!4 models

> show #!4 models

> show #!7 models

> hide #!7 models

> hide #!4 models

> show #!3 models

> volume flip #3

Opened cryosparc_P9_J635_008_volume_map_sharp.mrc z flip as #6, grid size
480,480,480, pixel 0.825, shown at step 1, values float32  

> open /home/pinkie/Documents/Charlotte/2024_01_28/fulmodel-v6-crosslinked.pdb

Chain information for fulmodel-v6-crosslinked.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
R | No description available  
  

> open /home/pinkie/Documents/Charlotte/2024_01_28/fullmodel-v5.pdb

Chain information for fullmodel-v5.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
R | No description available  
  

> hide #9-10 atoms

> show #9-10 cartoons

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> hide #10 models

> fitmap #9 inMap #6

Fit molecule fulmodel-v6-crosslinked.pdb (#9) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) using 19807 atoms  
average map value = 0.1322, steps = 48  
shifted from previous position = 0.00848  
rotated from previous position = 0.0222 degrees  
atoms outside contour = 7877, contour level = 0.093576  
  
Position of fulmodel-v6-crosslinked.pdb (#9) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) coordinates:  
Matrix rotation and translation  
0.99999993 -0.00034748 -0.00013386 0.09294722  
0.00034750 0.99999993 0.00010561 -0.08510450  
0.00013382 -0.00010566 0.99999999 0.00149379  
Axis -0.27290890 -0.34577439 0.89775320  
Axis point 239.58376669 271.68215520 0.00000000  
Rotation angle (degrees) 0.02217725  
Shift along axis 0.00540189  
  

> hide #9 models

> show #10 models

> fitmap #10 inMap #6

Fit molecule fullmodel-v5.pdb (#10) to map
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) using 19807 atoms  
average map value = 0.1121, steps = 152  
shifted from previous position = 10.8  
rotated from previous position = 6.89 degrees  
atoms outside contour = 9792, contour level = 0.093576  
  
Position of fullmodel-v5.pdb (#10) relative to
cryosparc_P9_J635_008_volume_map_sharp.mrc z flip (#6) coordinates:  
Matrix rotation and translation  
0.99762593 -0.02091198 -0.06561397 23.93517264  
0.01436000 0.99500528 -0.09878407 25.98670381  
0.06735202 0.09760733 0.99294336 -32.41050705  
Axis 0.81905399 -0.55453714 0.14710244  
Axis point 0.00000000 350.60177499 247.72967437  
Rotation angle (degrees) 6.88570607  
Shift along axis 0.42594157  
  

> show #9 models

> hide #!6 models

> hide #10 models

> show #10 models

> hide #10 models

> show #10 models

> hide #10 models

> show #10 models

> hide #10 models

> show #10 models

> hide #10 models

> show #10 models

> hide #10 models

> show #10 models

> show #!5 models

> show #9-10#!5 cartoons

> hide #!5 models

> show #!5 models

> hide #!5 models

> show #!5 models

> select add #5

23537 atoms, 23790 bonds, 1 pseudobond, 1735 residues, 3 models selected  

> help help:user

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.52174,-0.29947,0.79881,191.85,-0.34266,-0.78395,-0.5177,206.15,0.78126,-0.54383,0.3064,152.39,#4.2,1,-0.00058113,0.00045808,-0.80996,0.00058103,1,0.00021172,5.8066,-0.0004582,-0.00021146,1,0.83911

> select subtract #5

19807 atoms, 20027 bonds, 1225 residues, 1 model selected  

> hide #9 models

> hide #10 models

> show #!6 models

> fitmap #5 inMap #6

Fit molecule 5t35 (#5) to map cryosparc_P9_J635_008_volume_map_sharp.mrc z
flip (#6) using 3730 atoms  
average map value = 0.08285, steps = 112  
shifted from previous position = 5.2  
rotated from previous position = 3.59 degrees  
atoms outside contour = 2412, contour level = 0.093576  
  
Position of 5t35 (#5) relative to cryosparc_P9_J635_008_volume_map_sharp.mrc z
flip (#6) coordinates:  
Matrix rotation and translation  
-0.49489741 -0.35355994 0.79377070 195.33404698  
-0.33737792 -0.76363743 -0.55048525 209.06766347  
0.80078255 -0.54023443 0.25863887 152.81110365  
Axis 0.50252548 -0.34374169 0.79329049  
Axis point 48.43141862 138.03079969 0.00000000  
Rotation angle (degrees) 179.41561301  
Shift along axis 147.51865747  
  

> show #9 models

> show #10 models

> hide #!6 models

> hide #!5 models

> select #9/R

1432 atoms, 1452 bonds, 92 residues, 1 model selected  

> select clear

> select #9/R

1432 atoms, 1452 bonds, 92 residues, 1 model selected  

> color sel lime

> select clear

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J649_006_volume_map_sharp.mrc

Opened cryosparc_P9_J649_006_volume_map_sharp.mrc as #11, grid size
420,420,420, pixel 0.825, shown at level 0.0268, step 2, values float32  

> volume #11 level 0.09477

> volume #11 level 0.07304

> select add #11

3 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #11,0.79578,-0.21636,0.56562,-21.157,-0.2012,-0.9754,-0.090028,385.2,0.57118,-0.042161,-0.81974,208.32

> volume flip #11

Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #12, grid size
420,420,420, pixel 0.825, shown at step 1, values float32  

> select add #12

4 models selected  

> close #11

> ui mousemode right "translate selected models"

> view matrix models
> #12,0.79578,-0.21636,0.56562,-21.535,-0.2012,-0.9754,-0.090028,420.27,0.57118,-0.042161,-0.81974,256.69

> ui mousemode right "rotate selected models"

> view matrix models
> #12,-0.97755,0.059009,-0.20229,370.12,-0.055777,-0.99821,-0.021647,387.2,-0.20321,-0.0098776,0.97909,50.616

> ui mousemode right "translate selected models"

> view matrix models
> #12,-0.97755,0.059009,-0.20229,369.93,-0.055777,-0.99821,-0.021647,388.27,-0.20321,-0.0098776,0.97909,64.412

> view matrix models
> #12,-0.97755,0.059009,-0.20229,390.8,-0.055777,-0.99821,-0.021647,385.58,-0.20321,-0.0098776,0.97909,68.302

Must specify one map, got 0  

> show #!7 models

> hide #!7 models

> show #!6 models

> hide #!6 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 1 maps.  

> hide #!4.1 models

> hide #!4.2 models

> hide #4.3 models

> close #10

> fitmap #9 inMap #12

Fit molecule fulmodel-v6-crosslinked.pdb (#9) to map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#12) using 19807 atoms  
average map value = 0.1186, steps = 168  
shifted from previous position = 7.18  
rotated from previous position = 10.2 degrees  
atoms outside contour = 7210, contour level = 0.073036  
  
Position of fulmodel-v6-crosslinked.pdb (#9) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#12) coordinates:  
Matrix rotation and translation  
-0.99893072 -0.03543972 -0.02968888 383.81872944  
0.03672114 -0.99836564 -0.04379003 372.34530599  
-0.02808845 -0.04483342 0.99859951 -6.07997840  
Axis -0.01445423 -0.02217085 0.99964970  
Axis point 188.50734431 189.56827757 0.00000000  
Rotation angle (degrees) 177.93156998  
Shift along axis -19.88086512  
  

> select clear

> surface dust #12 size 8.25

> volume #12 level 0.04915

> volume #4.1.1.1 level 0.1137

> show #!4.1 models

> show #!4.2 models

> show #4.3 models

> hide #!4.2 models

> hide #4.3 models

> hide #!4.1 models

> show #!6 models

> hide #!6 models

> open 8b3i

Summary of feedback from opening 8b3i fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /N:1  
Atom H1 is not in the residue template for MET /U:1  
Atom H1 is not in the residue template for MET /a:1  
Atom H1 is not in the residue template for MET /d:1  
note | Fetching compressed mmCIF 8b3i from
http://files.rcsb.org/download/8b3i.cif  
  
8b3i title:  
CRL4CSA-E2-Ub (state 2) [more info...]  
  
Chain information for 8b3i #10  
---  
Chain | Description | UniProt  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN  
U | Ubiquitin | UBC_HUMAN  
a | DNA excision repair protein ERCC-8 | ERCC8_HUMAN  
d | DNA damage-binding protein 1 | DDB1_HUMAN  
e | Cullin-4A | CUL4A_HUMAN  
  
Non-standard residues in 8b3i #10  
---  
ZN — zinc ion  
  

> select #10/a

5627 atoms, 5686 bonds, 365 residues, 1 model selected  

> delete sel

> select #10/d

17196 atoms, 17351 bonds, 6 pseudobonds, 1096 residues, 2 models selected  

> delete sel

> ui tool show Matchmaker

> matchmaker #!10 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 1216.9  
RMSD between 161 pruned atom pairs is 1.160 angstroms; (across all 614 pairs:
19.630)  
  

> matchmaker #!10 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 1216.9  
RMSD between 161 pruned atom pairs is 1.160 angstroms; (across all 614 pairs:
19.630)  
  

> hide #!12 models

> hide #9 models

> hide #!4 models

> hide #!10 atoms

> show #!10 cartoons

> select #10/E:42-354

Nothing selected  

> select #10/e:42-354

5160 atoms, 5206 bonds, 313 residues, 1 model selected  

> delete sel

> show #9 models

> ui tool show Matchmaker

> matchmaker #!10 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 826.6  
RMSD between 150 pruned atom pairs is 1.050 angstroms; (across all 315 pairs:
4.185)  
  

> matchmaker #!10 to #9

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker fulmodel-v6-crosslinked.pdb, chain E (#9) with 8b3i, chain e (#10),
sequence alignment score = 826.6  
RMSD between 150 pruned atom pairs is 1.050 angstroms; (across all 315 pairs:
4.185)  
  

> show #!12 models

> hide #9 models

> show #9 models

> hide #!12 models

> open 6nyo

Summary of feedback from opening 6nyo fetched from pdb  
---  
note | Fetching compressed mmCIF 6nyo from
http://files.rcsb.org/download/6nyo.cif  
  
6nyo title:  
Crystal structure of a human Cdc34-ubiquitin thioester mimetic [more info...]  
  
Chain information for 6nyo #11  
---  
Chain | Description | UniProt  
A | Ubiquitin-conjugating enzyme E2 R2 | UB2R2_HUMAN  
E | Ubiquitin |  
  
Non-standard residues in 6nyo #11  
---  
EDO — 1,2-ethanediol (ethylene glycol)  
PO4 — phosphate ion  
U94 —
4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic
acid  
  

> ui tool show Matchmaker

> matchmaker #11 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8b3i, chain U (#10) with 6nyo, chain E (#11), sequence alignment
score = 312.7  
RMSD between 71 pruned atom pairs is 0.646 angstroms; (across all 76 pairs:
1.638)  
  

> matchmaker #11 to #10

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 8b3i, chain U (#10) with 6nyo, chain E (#11), sequence alignment
score = 312.7  
RMSD between 71 pruned atom pairs is 0.646 angstroms; (across all 76 pairs:
1.638)  
  

> show #!12 models

> hide #11 models

> hide #!10 models

> transparency #12.1 50

> volume #12 level 0.1357

> volume #12 level 0.09393

> show #!10 models

> hide #9 models

> volume #12 level 0.07005

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc

Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc as #13, grid
size 512,512,512, pixel 0.74, shown at level 0.0183, step 2, values float32  

> volume #13 level 0.08943

> hide #!10 models

> volume #13 level 0.04837

> surface dust #13 size 7.4

> volume #13 level 0.04837

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J846_005_volume_mask_refine.mrc

Opened cryosparc_P7_J846_005_volume_mask_refine.mrc as #14, grid size
512,512,512, pixel 0.74, shown at level 0.959, step 2, values float32  

> ui mousemode right "map eraser"

[Repeated 1 time(s)]

Can only have one displayed volume when erasing  

[Repeated 11 time(s)]

> volume erase #13 center 210.44,248.48,205.99 radius 24.248

Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy as #16,
grid size 512,512,512, pixel 0.74, shown at step 1, values float32  

> volume erase #16 center 141.76,228.51,179.62 radius 24.248

> ui mousemode right "map eraser"

[Repeated 1 time(s)]

> volume gaussian #16

Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy gaussian as
#17, grid size 512,512,512, pixel 0.74, shown at step 1, values float32  

> volume #17 level 0.02761

> close #17

> volume gaussian #16 sDev 3

Opened OPENunbinnedcryosparc_P7_J846_005_volume_map_sharp.mrc copy gaussian as
#17, grid size 512,512,512, pixel 0.74, shown at step 1, values float32  

> surface dust #16 size 7.4

> save /home/pinkie/Documents/Charlotte/2024_01_28/J846-edited.mrc models #16

> close #17

> open /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P7_J852_mask.mrc

Opened cryosparc_P7_J852_mask.mrc as #17, grid size 512,512,512, pixel 0.74,
shown at level 1, step 2, values float32  

> volume #17 level 0.9908

> close #17

> close #16

> close #14

> close #13

> close #1

> volume #7 level 0.07099

> close #3

> volume #12 level 0.04968

> show #9 models

> hide #!12 models

> show #11 models

> select #11/E

705 atoms, 628 bonds, 161 residues, 1 model selected  

> color sel yellow

> select clear

> show #!12 models

> hide #!12 models

> hide #9 models

> show #!8 models

> show #9 models

> hide #9 models

> hide #11 models

> view

> show #11 models

> ui mousemode right translate

> ui mousemode right select

> select clear

> select #11/E:34

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

> show sel atoms

> color sel orange

> select clear

> hide #!8 models

> show #!8 models

> ui tool show Matchmaker

> matchmaker #!8 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nyo, chain E (#11) with 6ttu, chain U (#8), sequence alignment
score = 340  
RMSD between 70 pruned atom pairs is 0.714 angstroms; (across all 75 pairs:
1.524)  
  

> matchmaker #!8 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nyo, chain E (#11) with 6ttu, chain U (#8), sequence alignment
score = 340  
RMSD between 70 pruned atom pairs is 0.714 angstroms; (across all 75 pairs:
1.524)  
  

> show #9 models

Drag select of 27 residues, 1 atoms, 4 bonds  

> select clear

> ui mousemode right translate

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> color (#9 & sel) orange red

> select clear

> hide #11 models

> open 6ttu

6ttu title:  
Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution:
NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 [more info...]  
  
Chain information for 6ttu #1  
---  
Chain | Description | UniProt  
C | Cullin-1 | CUL1_HUMAN  
D | Ubiquitin-conjugating enzyme E2 D2 | UB2D2_HUMAN  
I | CYS-LYS-LYS-ALA-ARG-HIS-ASP-SEP-GLY |  
N | NEDD8 | NEDD8_HUMAN  
R | E3 ubiquitin-protein ligase RBX1 | RBX1_HUMAN  
S | S-phase kinase-associated protein 1 | SKP1_HUMAN  
T | F-box/WD repeat-containing protein 1A | FBW1A_HUMAN  
U | Polyubiquitin-C | UBC_HUMAN  
  
Non-standard residues in 6ttu #1  
---  
ZN — zinc ion  
  

> hide #!8 models

> show #!10 models

> hide #!1 models

> show #11 models

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> select sequence YGH

92 atoms, 94 bonds, 6 residues, 2 models selected  

> select clear

> show #!12 models

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/UBE2R1AF-P49427-F1-model_v4.pdb

UBE2R1AF-P49427-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
(P49427) [more info...]  
  
Chain information for UBE2R1AF-P49427-F1-model_v4.pdb #3  
---  
Chain | Description | UniProt  
A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
  

> ui tool show Matchmaker

> matchmaker #3 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nyo, chain A (#11) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 920.3  
RMSD between 162 pruned atom pairs is 1.029 angstroms; (across all 188 pairs:
1.823)  
  

> matchmaker #3 to #11

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6nyo, chain A (#11) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 920.3  
RMSD between 162 pruned atom pairs is 1.029 angstroms; (across all 188 pairs:
1.823)  
  

> volume #12 level 0.02057

> volume #12 level 0.04386

> hide #!10 models

> hide #!12 models

> hide #11 models

> select #9/R

1432 atoms, 1452 bonds, 92 residues, 1 model selected  

> delete sel

> show #11 models

> hide #11 models

> show #!8 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> show #!1 models

> show #!8 models

> ui tool show Matchmaker

> matchmaker #!1 to #8

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ttu, chain D (#8) with 6ttu, chain D (#1), sequence alignment
score = 782.4  
RMSD between 146 pruned atom pairs is 0.000 angstroms; (across all 146 pairs:
0.000)  
  

> select add #1

12746 atoms, 12974 bonds, 25 pseudobonds, 1607 residues, 3 models selected  

> show sel cartoons

> hide sel atoms

> select clear

> select #1/I

58 atoms, 57 bonds, 1 pseudobond, 9 residues, 2 models selected  

> delete sel

> select #1/T

3085 atoms, 3146 bonds, 2 pseudobonds, 394 residues, 2 models selected  

> delete sel

> select #1/S

891 atoms, 903 bonds, 3 pseudobonds, 123 residues, 2 models selected  

> delete sel

> select #1/C

5728 atoms, 5820 bonds, 6 pseudobonds, 701 residues, 2 models selected  

> delete sel

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

> show #11 models

> hide #11 models

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 50, in   
data[0] == pself.attr_name and (setattr(pself, "value", pself.get_attribute())  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
Error processing trigger "setting changed":  
AttributeError: 'NoneType' object has no attribute 'setChecked'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/ui/options/options.py", line 342, in set_value  
self.__button_group.button(self.values.index(value)).setChecked(True)  
  
See log for complete Python traceback.  
  

> matchmaker #3 to #1/D pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 6ttu, chain D (#1) with UBE2R1AF-P49427-F1-model_v4.pdb, chain A
(#3), sequence alignment score = 338.9  
RMSD between 135 pruned atom pairs is 0.960 angstroms; (across all 145 pairs:
1.521)  
  

> select #1/D

1135 atoms, 1171 bonds, 146 residues, 1 model selected  

> delete sel

> hide #!8 models

> select add #9

18375 atoms, 18575 bonds, 1133 residues, 1 model selected  

> select add #3

20262 atoms, 20513 bonds, 1369 residues, 2 models selected  

> select add #1

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 5 models selected  

> save /home/pinkie/Documents/Charlotte/2024_01_28/full-model-7.pdb
> selectedOnly true

> select clear

> select add #1

1849 atoms, 1876 bonds, 13 pseudobonds, 234 residues, 3 models selected  

> select add #3

3736 atoms, 3814 bonds, 13 pseudobonds, 470 residues, 4 models selected  

> select add #9

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 5 models selected  

> combine sel

Remapping chain ID 'A' in fulmodel-v6-crosslinked.pdb #9 to 'F'  

> save /home/pinkie/Documents/Charlotte/2024_01_28/full-model-7.pdb models #13

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 58 residues in model #13 to IUPAC-IUB
standards.  

> select clear

> show #!12 models

> hide #!12 models

> clipper associate #12 toModel #13

Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #13.1.1.1, grid
size 420,420,420, pixel 0.825, shown at step 1, values float32  

> show #!7 models

> hide #!7 models

> select add #13.2

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 8 models selected  

> fitmap #13.2 inMap #13.1.1.1

Fit molecule combination (#13.2) to map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
atoms  
average map value = 0.05014, steps = 396  
shifted from previous position = 23.4  
rotated from previous position = 24.1 degrees  
atoms outside contour = 19566, contour level = 0.05014  
  
Position of combination (#13.2) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates:  
Matrix rotation and translation  
0.92317061 -0.20312451 0.32633796 -11.17355132  
0.24869275 0.96296817 -0.10413559 -33.51889854  
-0.29310057 0.17729280 0.93949950 15.03016877  
Axis 0.34458025 0.75843906 0.55320398  
Axis point 84.24190480 0.00000000 31.94318234  
Rotation angle (degrees) 24.10210987  
Shift along axis -20.95747771  
  

> hide #9 models

> hide #3 models

> hide #!1 models

> volume #!13.1.1.1 style surface

> select add #13.1

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 13 models selected  

> select add #13.2

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 13 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #13.1,-0.98269,-0.1026,-0.15424,429.7,0.10866,-0.99358,-0.031368,347.81,-0.15003,-0.047586,0.98753,39.267,#13.2,-0.8875,0.073459,-0.45492,441.8,-0.13759,-0.98442,0.10946,379.43,-0.43979,0.15973,0.88378,57.381

> select add #13

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 15 models selected  

> select subtract #13.3

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 14 models selected  

> hide #!13 models

> show #!13 models

> view matrix models
> #13,0.81208,0.54878,0.19838,-100.24,-0.5225,0.8352,-0.17155,164.87,-0.25983,0.035658,0.96499,51.139

> select clear

> select add #13.1

5 models selected  

> view matrix models
> #13.1,0.83139,-0.40689,-0.37845,195.35,0.35956,0.91317,-0.19191,-14.667,0.42368,0.023477,0.90551,-63.182

> ui mousemode right "translate selected models"

> view matrix models
> #13.1,0.83139,-0.40689,-0.37845,187.29,0.35956,0.91317,-0.19191,-11.823,0.42368,0.023477,0.90551,-54.397

> fitmap #13.2 inMap #13.1.1.1

Fit molecule combination (#13.2) to map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
atoms  
average map value = 0.1116, steps = 280  
shifted from previous position = 5.36  
rotated from previous position = 24.3 degrees  
atoms outside contour = 8152, contour level = 0.05014  
  
Position of combination (#13.2) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates:  
Matrix rotation and translation  
-0.75913436 0.36618451 -0.53816720 379.62642684  
-0.25697956 -0.92820081 -0.26908132 464.97537207  
-0.59806064 -0.06597091 0.79873106 150.13087714  
Axis 0.30860342 0.09100135 -0.94682769  
Axis point 255.69788645 206.24934727 0.00000000  
Rotation angle (degrees) 160.78705671  
Shift along axis 17.31932933  
  

> select clear

> surface dust #13.1.1.1 size 8.25

> view matrix models
> #13.2,-0.75913,0.36618,-0.53817,398.64,-0.25698,-0.9282,-0.26908,469.57,-0.59806,-0.065971,0.79873,125.43

> view matrix models
> #13.2,-0.75913,0.36618,-0.53817,381.57,-0.25698,-0.9282,-0.26908,467.93,-0.59806,-0.065971,0.79873,146.56

> fitmap #13.2 inMap #13.1.1.1

Fit molecule combination (#13.2) to map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
atoms  
average map value = 0.1336, steps = 120  
shifted from previous position = 5.13  
rotated from previous position = 0.544 degrees  
atoms outside contour = 12403, contour level = 0.05014  
  
Position of combination (#13.2) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates:  
Matrix rotation and translation  
-0.75493092 0.36668844 -0.54370847 379.59746213  
-0.25313255 -0.92775240 -0.27422507 464.92394264  
-0.60498200 -0.06939067 0.79320975 153.04464514  
Axis 0.31240962 0.09345325 -0.94533947  
Axis point 256.39528686 206.66536567 0.00000000  
Rotation angle (degrees) 160.86289101  
Shift along axis 17.35941085  
  

> select clear

> volume #!13.1.1.1 style mesh

> isolde sim start sel

ISOLDE: stopped sim  

> select clear

[Repeated 1 time(s)]Fetching CCD MET_LL from http://ligand-
expo.rcsb.org/reports/M/MET_LL/MET_LL.cif  
Fetching CCD MET_LEO2 from http://ligand-
expo.rcsb.org/reports/M/MET_LEO2/MET_LEO2.cif  
Fetching CCD MET_LFZW from http://ligand-
expo.rcsb.org/reports/M/MET_LFZW/MET_LFZW.cif  
Fetching CCD FME from http://ligand-expo.rcsb.org/reports/F/FME/FME.cif  
Fetching CCD AME from http://ligand-expo.rcsb.org/reports/A/AME/AME.cif  
Fetching CCD ALA_LL from http://ligand-
expo.rcsb.org/reports/A/ALA_LL/ALA_LL.cif  
Fetching CCD SER_LL_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LL_DHG/SER_LL_DHG.cif  
Fetching CCD SER_LL from http://ligand-
expo.rcsb.org/reports/S/SER_LL/SER_LL.cif  
Fetching CCD ALA_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ALA_LEO2/ALA_LEO2.cif  
Fetching CCD SER_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LSN3_DHG/SER_LSN3_DHG.cif  
Fetching CCD ALA_LFZW from http://ligand-
expo.rcsb.org/reports/A/ALA_LFZW/ALA_LFZW.cif  
Fetching CCD PRO_LL from http://ligand-
expo.rcsb.org/reports/P/PRO_LL/PRO_LL.cif  
Fetching CCD CYS_LL_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LL_DHG/CYS_LL_DHG.cif  
Fetching CCD THR_LL_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LL_DHG1/THR_LL_DHG1.cif  
Fetching CCD SER_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2_DHG/SER_LEO2_DHG.cif  
Fetching CCD CYS_LL from http://ligand-
expo.rcsb.org/reports/C/CYS_LL/CYS_LL.cif  
Fetching CCD THR_LL from http://ligand-
expo.rcsb.org/reports/T/THR_LL/THR_LL.cif  
Fetching CCD VAL_LL from http://ligand-
expo.rcsb.org/reports/V/VAL_LL/VAL_LL.cif  
Fetching CCD SER_LEO2 from http://ligand-
expo.rcsb.org/reports/S/SER_LEO2/SER_LEO2.cif  
Fetching CCD CYS_LSN3_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LSN3_DHG/CYS_LSN3_DHG.cif  
Fetching CCD THR_LSN3_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LSN3_DHG1/THR_LSN3_DHG1.cif  
Fetching CCD SER_LFZW_DHG from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW_DHG/SER_LFZW_DHG.cif  
Fetching CCD SER_LFZW from http://ligand-
expo.rcsb.org/reports/S/SER_LFZW/SER_LFZW.cif  
Fetching CCD PCA from http://ligand-expo.rcsb.org/reports/P/PCA/PCA.cif  
Fetching CCD ASP_LL_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LL_DHD2/ASP_LL_DHD2.cif  
Fetching CCD ASN_LL from http://ligand-
expo.rcsb.org/reports/A/ASN_LL/ASN_LL.cif  
Fetching CCD ASP_LL from http://ligand-
expo.rcsb.org/reports/A/ASP_LL/ASP_LL.cif  
Fetching CCD PRO_LEO2 from http://ligand-
expo.rcsb.org/reports/P/PRO_LEO2/PRO_LEO2.cif  
Fetching CCD HY3 from http://ligand-expo.rcsb.org/reports/H/HY3/HY3.cif  
Fetching CCD CYS_LEO2_DHG from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2_DHG/CYS_LEO2_DHG.cif  
Fetching CCD ASP_LSN3_DHD2 from http://ligand-
expo.rcsb.org/reports/A/ASP_LSN3_DHD2/ASP_LSN3_DHD2.cif  
Fetching CCD AYA from http://ligand-expo.rcsb.org/reports/A/AYA/AYA.cif  
Fetching CCD THR_LEO2_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2_DHG1/THR_LEO2_DHG1.cif  
Fetching CCD ILE_LL from http://ligand-
expo.rcsb.org/reports/I/ILE_LL/ILE_LL.cif  
Fetching CCD LEU_LL from http://ligand-
expo.rcsb.org/reports/L/LEU_LL/LEU_LL.cif  
Fetching CCD CYS_LEO2 from http://ligand-
expo.rcsb.org/reports/C/CYS_LEO2/CYS_LEO2.cif  
Fetching CCD THR_LEO2 from http://ligand-
expo.rcsb.org/reports/T/THR_LEO2/THR_LEO2.cif  
Fetching CCD VAL_LEO2 from http://ligand-
expo.rcsb.org/reports/V/VAL_LEO2/VAL_LEO2.cif  
Fetching CCD CSO from http://ligand-expo.rcsb.org/reports/C/CSO/CSO.cif  
Fetching CCD PRO_LFZW from http://ligand-
expo.rcsb.org/reports/P/PRO_LFZW/PRO_LFZW.cif  
Fetching CCD THR_LFZW_DHG1 from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW_DHG1/THR_LFZW_DHG1.cif  
Fetching CCD ORN from http://ligand-expo.rcsb.org/reports/O/ORN/ORN.cif  
Fetching CCD CYS_LFZW from http://ligand-
expo.rcsb.org/reports/C/CYS_LFZW/CYS_LFZW.cif  
Fetching CCD THR_LFZW from http://ligand-
expo.rcsb.org/reports/T/THR_LFZW/THR_LFZW.cif  
Fetching CCD VAL_LFZW from http://ligand-
expo.rcsb.org/reports/V/VAL_LFZW/VAL_LFZW.cif  
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif  
Fetching CCD ARG_LL from http://ligand-
expo.rcsb.org/reports/A/ARG_LL/ARG_LL.cif  
Fetching CCD ARG_LL_DHH22 from http://ligand-
expo.rcsb.org/reports/A/ARG_LL_DHH22/ARG_LL_DHH22.cif  
Fetching CCD ARG_LEO2 from http://ligand-
expo.rcsb.org/reports/A/ARG_LEO2/ARG_LEO2.cif  
Fetching CCD NMM from http://ligand-expo.rcsb.org/reports/N/NMM/NMM.cif  
Fetching CCD ARG_LFZW from http://ligand-
expo.rcsb.org/reports/A/ARG_LFZW/ARG_LFZW.cif  
Fetching CCD 2MR from http://ligand-expo.rcsb.org/reports/2/2MR/2MR.cif  
Fetching CCD DA2 from http://ligand-expo.rcsb.org/reports/D/DA2/DA2.cif  
Fetching CCD AAG from http://ligand-expo.rcsb.org/reports/A/AAG/AAG.cif  
Fetching CCD N7P from http://ligand-expo.rcsb.org/reports/N/N7P/N7P.cif  
Fetching CCD LEU_LEO2 from http://ligand-
expo.rcsb.org/reports/L/LEU_LEO2/LEU_LEO2.cif  
Fetching CCD LEU_LFZW from http://ligand-
expo.rcsb.org/reports/L/LEU_LFZW/LEU_LFZW.cif  
Fetching CCD PHE_LL from http://ligand-
expo.rcsb.org/reports/P/PHE_LL/PHE_LL.cif  
Fetching CCD LAY from http://ligand-expo.rcsb.org/reports/L/LAY/LAY.cif  
Fetching CCD ILE_LEO2 from http://ligand-
expo.rcsb.org/reports/I/ILE_LEO2/ILE_LEO2.cif  
Fetching CCD ILE_LFZW from http://ligand-
expo.rcsb.org/reports/I/ILE_LFZW/ILE_LFZW.cif  

> fitmap #13.2 inMap #13.1.1.1

Fit molecule combination (#13.2) to map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) using 22111
atoms  
average map value = 0.07731, steps = 320  
shifted from previous position = 20.7  
rotated from previous position = 33.8 degrees  
atoms outside contour = 11736, contour level = 0.05014  
  
Position of combination (#13.2) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#13.1.1.1) coordinates:  
Matrix rotation and translation  
-0.97583225 -0.05210471 -0.21221809 418.79073088  
0.06601319 -0.99607381 -0.05898489 373.10247849  
-0.20831149 -0.07156855 0.97544055 32.30370160  
Axis -0.10587804 -0.03286985 0.99383571  
Axis point 205.54590673 193.31244448 0.00000000  
Rotation angle (degrees) 176.59317612  
Shift along axis -24.49999338  
  

> isolde sim start sel

ISOLDE: stopped sim  

> select #13.2/F

1835 atoms, 1858 bonds, 114 residues, 1 model selected  

> select #13.2/B

2615 atoms, 2648 bonds, 160 residues, 1 model selected  

> select #13.2/A

1887 atoms, 1938 bonds, 236 residues, 1 model selected  
Please select a single atom!  

> select clear

[Repeated 2 time(s)]Please select a single atom!  

> isolde shorthand
    
    
    Initialising ISOLDE-specific command aliases:
    Alias	Equivalent full command
    -------------------------------------------------
    st	isolde step {arguments}
    aw	isolde add water {arguments}
    awsf	isolde add water {arguments} sim false
    al	isolde add ligand {arguments}
    aa	isolde add aa $1 sel {arguments}
    ht	isolde mod his sel {arguments}
    so	setattr sel atoms occupancy {arguments}
    ab	isolde adjust bfactors {arguments}
    ss	isolde sim start sel
    rt	isolde release torsions sel {arguments}
    rd	isolde release distances sel {arguments}
    ra	rd; rt
    pf	isolde pepflip sel
    cf	isolde cisflip sel
    cbb	color bfactor {arguments}
    cbo	color byattr occupancy {arguments}
    cbc	color {arguments} bychain; color {arguments} byhet
    cs	clipper set contourSensitivity {arguments}
    

  

> addh

Summary of feedback from adding hydrogens to multiple structures  
---  
warnings | Not adding hydrogens to 5t35 #5/A LYS 349 CB because it is missing
heavy-atom bond partners  
Not adding hydrogens to 5t35 #5/A LYS 362 CD because it is missing heavy-atom
bond partners  
Not adding hydrogens to 5t35 #5/A LYS 367 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 5t35 #5/A LYS 395 CB because it is missing heavy-atom
bond partners  
Not adding hydrogens to 5t35 #5/A ARG 413 CB because it is missing heavy-atom
bond partners  
33 messages similar to the above omitted  
notes | Termini for 5t35 (#5) chain A determined from SEQRES records  
Termini for 5t35 (#5) chain B determined from SEQRES records  
Termini for 5t35 (#5) chain C determined from SEQRES records  
Termini for 5t35 (#5) chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: 5t35 #5/B MET 1, 5t35 #5/C
MET 16  
Chain-initial residues that are not actual N termini: 5t35 #5/A LYS 349, 5t35
#5/C ASN 58, 5t35 #5/D PRO 61  
Chain-final residues that are actual C termini: 5t35 #5/B LYS 104, 5t35 #5/C
CYS 112  
Chain-final residues that are not actual C termini: 5t35 #5/A ASP 459, 5t35
#5/C SER 47, 5t35 #5/D GLN 209  
579 hydrogen bonds  
Adding 'H' to 5t35 #5/A LYS 349  
Adding 'H' to 5t35 #5/C ASN 58  
5t35 #5/A ASP 459 is not terminus, removing H atom from 'C'  
5t35 #5/D GLN 209 is not terminus, removing H atom from 'C'  
Termini for 6ttu (#8) chain N determined from SEQRES records  
Termini for 6ttu (#8) chain R determined from SEQRES records  
Termini for 6ttu (#8) chain D determined from SEQRES records  
Termini for 6ttu (#8) chain U determined from SEQRES records  
Chain-initial residues that are actual N termini: 6ttu #8/N SER 0, 6ttu #8/U
MET 1  
Chain-initial residues that are not actual N termini: 6ttu #8/R ASP 40, 6ttu
#8/R GLU 67, 6ttu #8/D ALA 2  
Chain-final residues that are actual C termini: 6ttu #8/N GLY 76, 6ttu #8/D
MET 147  
Chain-final residues that are not actual C termini: 6ttu #8/R ASN 59, 6ttu
#8/R GLN 104, 6ttu #8/U GLY 75  
Missing OXT added to C-terminal residue 6ttu #8/N GLY 76  
Missing OXT added to C-terminal residue 6ttu #8/D MET 147  
224 hydrogen bonds  
Adding 'H' to 6ttu #8/R ASP 40  
Adding 'H' to 6ttu #8/R GLU 67  
Adding 'H' to 6ttu #8/D ALA 2  
6ttu #8/R GLN 104 is not terminus, removing H atom from 'C'  
6ttu #8/U GLY 75 is not terminus, removing H atom from 'C'  
Termini for fullmodel-v5.pdb (#4.2) chain A determined from SEQRES records  
Termini for fullmodel-v5.pdb (#4.2) chain B determined from SEQRES records  
Termini for fullmodel-v5.pdb (#4.2) chain C determined from SEQRES records  
Termini for fullmodel-v5.pdb (#4.2) chain D determined from SEQRES records  
Termini for fullmodel-v5.pdb (#4.2) chain E determined from SEQRES records  
1 messages similar to the above omitted  
Chain-initial residues that are actual N termini: fullmodel-v5.pdb #4.2/B MET
54, fullmodel-v5.pdb #4.2/C MET 1, fullmodel-v5.pdb #4.2/D ALA 16,
fullmodel-v5.pdb #4.2/E MET 1  
Chain-initial residues that are not actual N termini: fullmodel-v5.pdb #4.2/A
SER 347, fullmodel-v5.pdb #4.2/R LYS 20  
Chain-final residues that are actual C termini: fullmodel-v5.pdb #4.2/A GLU
460, fullmodel-v5.pdb #4.2/B ASP 213, fullmodel-v5.pdb #4.2/C LYS 104,
fullmodel-v5.pdb #4.2/D CYS 112  
Chain-final residues that are not actual C termini: fullmodel-v5.pdb #4.2/E
GLN 658, fullmodel-v5.pdb #4.2/R HIS 108  
1466 hydrogen bonds  
fullmodel-v5.pdb #4.2/E GLN 658 is not terminus, removing H atom from 'C'  
Termini for fulmodel-v6-crosslinked.pdb (#9) chain A determined from SEQRES
records  
Termini for fulmodel-v6-crosslinked.pdb (#9) chain B determined from SEQRES
records  
Termini for fulmodel-v6-crosslinked.pdb (#9) chain C determined from SEQRES
records  
Termini for fulmodel-v6-crosslinked.pdb (#9) chain D determined from SEQRES
records  
Termini for fulmodel-v6-crosslinked.pdb (#9) chain E determined from SEQRES
records  
Chain-initial residues that are actual N termini: fulmodel-v6-crosslinked.pdb
#9/B MET 54, fulmodel-v6-crosslinked.pdb #9/C MET 1,
fulmodel-v6-crosslinked.pdb #9/D ALA 16, fulmodel-v6-crosslinked.pdb #9/E MET
1  
Chain-initial residues that are not actual N termini:
fulmodel-v6-crosslinked.pdb #9/A SER 347  
Chain-final residues that are actual C termini: fulmodel-v6-crosslinked.pdb
#9/A GLU 460, fulmodel-v6-crosslinked.pdb #9/B ASP 213,
fulmodel-v6-crosslinked.pdb #9/C LYS 104, fulmodel-v6-crosslinked.pdb #9/D CYS
112  
Chain-final residues that are not actual C termini:
fulmodel-v6-crosslinked.pdb #9/E GLN 658  
1353 hydrogen bonds  
fulmodel-v6-crosslinked.pdb #9/E GLN 658 is not terminus, removing H atom from
'C'  
Termini for 8b3i (#10) chain D determined from SEQRES records  
Termini for 8b3i (#10) chain N determined from SEQRES records  
Termini for 8b3i (#10) chain R determined from SEQRES records  
Termini for 8b3i (#10) chain U determined from SEQRES records  
Termini for 8b3i (#10) chain e determined from SEQRES records  
Chain-initial residues that are actual N termini: 8b3i #10/N MET 1, 8b3i #10/U
MET 1  
Chain-initial residues that are not actual N termini: 8b3i #10/D ALA 2, 8b3i
#10/R LYS 19, 8b3i #10/R GLU 67, 8b3i #10/e PRO 355, 8b3i #10/e ARG 692  
Chain-final residues that are actual C termini: 8b3i #10/D MET 147, 8b3i #10/N
GLY 76, 8b3i #10/U GLY 76, 8b3i #10/e ALA 759  
Chain-final residues that are not actual C termini: 8b3i #10/R ASN 59, 8b3i
#10/R GLN 104, 8b3i #10/e ILE 672  
Missing OXT added to C-terminal residue 8b3i #10/D MET 147  
Missing OXT added to C-terminal residue 8b3i #10/N GLY 76  
Missing OXT added to C-terminal residue 8b3i #10/U GLY 76  
500 hydrogen bonds  
Adding 'H' to 8b3i #10/D ALA 2  
Adding 'H' to 8b3i #10/R LYS 19  
Adding 'H' to 8b3i #10/R GLU 67  
Adding 'H' to 8b3i #10/e ARG 692  
8b3i #10/R GLN 104 is not terminus, removing H atom from 'C'  
Termini for 6nyo (#11) chain A determined from SEQRES records  
Termini for 6nyo (#11) chain E determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: 6nyo #11/A GLN 5, 6nyo
#11/E SER -1  
Chain-final residues that are actual C termini: 6nyo #11/E GLY 76  
Chain-final residues that are not actual C termini: 6nyo #11/A ILE 192  
1134 hydrogen bonds  
Adding 'H' to 6nyo #11/A GLN 5  
Adding 'H' to 6nyo #11/E SER -1  
6nyo #11/A ILE 192 is not terminus, removing H atom from 'C'  
Termini for 6ttu (#1) chain N determined from SEQRES records  
Termini for 6ttu (#1) chain R determined from SEQRES records  
Termini for 6ttu (#1) chain U determined from SEQRES records  
Chain-initial residues that are actual N termini: 6ttu #1/N SER 0, 6ttu #1/U
MET 1  
Chain-initial residues that are not actual N termini: 6ttu #1/R LYS 19, 6ttu
#1/R GLU 67  
Chain-final residues that are actual C termini: 6ttu #1/N GLY 76  
Chain-final residues that are not actual C termini: 6ttu #1/R ASN 59, 6ttu
#1/R GLN 104, 6ttu #1/U GLY 75  
Missing OXT added to C-terminal residue 6ttu #1/N GLY 76  
126 hydrogen bonds  
Adding 'H' to 6ttu #1/R LYS 19  
Adding 'H' to 6ttu #1/R GLU 67  
6ttu #1/R GLN 104 is not terminus, removing H atom from 'C'  
6ttu #1/U GLY 75 is not terminus, removing H atom from 'C'  
Termini for UBE2R1AF-P49427-F1-model_v4.pdb (#3) chain A determined from
SEQRES records  
Chain-initial residues that are actual N termini:
UBE2R1AF-P49427-F1-model_v4.pdb #3/A MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:
UBE2R1AF-P49427-F1-model_v4.pdb #3/A SER 236  
Chain-final residues that are not actual C termini:  
177 hydrogen bonds  
Termini for combination (#13.2) chain N determined from SEQRES records  
Termini for combination (#13.2) chain R determined from SEQRES records  
Termini for combination (#13.2) chain U determined from SEQRES records  
Termini for combination (#13.2) chain A determined from SEQRES records  
Termini for combination (#13.2) chain F determined from SEQRES records  
4 messages similar to the above omitted  
Chain-initial residues that are actual N termini: combination #13.2/N SER 0,
combination #13.2/U MET 1, combination #13.2/A MET 1, combination #13.2/B MET
54, combination #13.2/C MET 1, combination #13.2/D ALA 16, combination #13.2/E
MET 1  
Chain-initial residues that are not actual N termini: combination #13.2/R LYS
19, combination #13.2/R GLU 67, combination #13.2/F SER 347  
Chain-final residues that are actual C termini: combination #13.2/N GLY 76,
combination #13.2/A SER 236, combination #13.2/F GLU 460, combination #13.2/B
ASP 213, combination #13.2/C LYS 104, combination #13.2/D CYS 112  
Chain-final residues that are not actual C termini: combination #13.2/R ASN
59, combination #13.2/R GLN 104, combination #13.2/U GLY 75, combination
#13.2/E GLN 658  
Missing OXT added to C-terminal residue combination #13.2/N GLY 76  
1674 hydrogen bonds  
Adding 'H' to combination #13.2/R LYS 19  
Adding 'H' to combination #13.2/R GLU 67  
combination #13.2/R GLN 104 is not terminus, removing H atom from 'C'  
combination #13.2/U GLY 75 is not terminus, removing H atom from 'C'  
combination #13.2/E GLN 658 is not terminus, removing H atom from 'C'  
16651 hydrogens added  
  

> select clear

> isolde sim start sel

ISOLDE: started sim  

> select clear

> dhide sideonly

Unknown command: dhide sideonly  

> dhide sideonly

Unknown command: dhide sideonly  

> hide sideonly

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hide sideonly

> hide ~@CA

> select clear

> select #13.2/N

1249 atoms, 1254 bonds, 77 residues, 1 model selected  

> color (#!13.2 & sel) cyan

> select clear

[Repeated 1 time(s)]

> delete sel

> select #13.2/A:180-218

579 atoms, 586 bonds, 39 residues, 1 model selected  

> delete sel

> isolde sim start sel

ISOLDE: started sim  

> select clear

[Repeated 1 time(s)]

> ui mousemode right "isolde tug atom"

> ui mousemode right "isolde tug residue"

> ui mousemode right "isolde tug atom"

[Repeated 1 time(s)]

> isolde sim resume

> select #13.2/R:19-37

345 atoms, 351 bonds, 17 pseudobonds, 19 residues, 2 models selected  

> delete sel

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> hide ~@CA

> ui mousemode right translate

> isolde sim start sel

ISOLDE: started sim  

> ui mousemode right translate

> isolde sim pause

> select clear

> select add #13

24624 atoms, 24886 bonds, 1169 pseudobonds, 1527 residues, 21 models selected  

> isolde sim resume

> isolde sim pause

> select clear

> isolde sim stop

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 56 residues in model #13.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> save /home/pinkie/Documents/Charlotte/2024_01_28/full-model-9-isoldeatt1.pdb
> models #13

> open /home/pinkie/Documents/Charlotte/2024_01_28/full-model-9-isoldeatt1.pdb

full-model-9-isoldeatt1.pdb title:  
Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
(P49427) [more info...]  
  
Chain information for full-model-9-isoldeatt1.pdb #12  
---  
Chain | Description | UniProt  
A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
B | No description available |  
C | No description available |  
D | No description available |  
E | No description available |  
F | No description available |  
N | No description available |  
R | No description available |  
U | No description available |  
  
Non-standard residues in full-model-9-isoldeatt1.pdb #12  
---  
ZN — (ZN)  
  

> select add #12

24624 atoms, 24886 bonds, 13 pseudobonds, 1527 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> hide #!13 models

> hide #!13.1 models

> hide #!13.2 models

> hide #13.3 models

> show #11 models

> hide #11 models

> show #9 models

> hide #9 models

> open /home/pinkie/Documents/Charlotte/2024_01_28/full-model-7.pdb

full-model-7.pdb title:  
Alphafold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 R1
(P49427) [more info...]  
  
Chain information for full-model-7.pdb #14  
---  
Chain | Description | UniProt  
A | ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
B | No description available |  
C | No description available |  
D | No description available |  
E | No description available |  
F | No description available |  
N | No description available |  
R | No description available |  
U | No description available |  
  
Non-standard residues in full-model-7.pdb #14  
---  
ZN — (ZN)  
  

> select add #14

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #14,-0.76775,-0.61838,0.16783,439.68,0.61794,-0.78383,-0.061302,262.94,0.16946,0.056645,0.98391,-41.6

> ui mousemode right "translate selected models"

> view matrix models
> #14,-0.76775,-0.61838,0.16783,414.71,0.61794,-0.78383,-0.061302,236.59,0.16946,0.056645,0.98391,-67.689

> show #!13.1 models

> ui mousemode right "translate selected atoms"

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 2 atomic models, 0 maps.  

> hide #!12 models

> show #!13.2 models

> hide #!13.2 models

> show #13.3 models

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.  

> hide #13.3 models

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J659_007_volume_map.mrc

Opened cryosparc_P9_J659_007_volume_map.mrc as #15, grid size 480,480,480,
pixel 0.825, shown at level 0.00707, step 2, values float32  

> close #15

> select clear

> select add #14

22111 atoms, 22389 bonds, 13 pseudobonds, 1603 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #13.2/A:177-236

51 atoms, 50 bonds, 3 residues, 1 model selected  

> delete sel

> select #14/A:177-236

465 atoms, 473 bonds, 60 residues, 1 model selected  

> delete sel

> select #14/R:19-37

170 atoms, 176 bonds, 19 residues, 1 model selected  

> delete sel

> open 7ojx

Summary of feedback from opening 7ojx fetched from pdb  
---  
notes | Fetching compressed mmCIF 7ojx from
http://files.rcsb.org/download/7ojx.cif  
Fetching CCD ME7 from http://ligand-expo.rcsb.org/reports/M/ME7/ME7.cif  
  
7ojx title:  
E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for
K48-linked Ub chain synthesis [more info...]  
  
Chain information for 7ojx #15  
---  
Chain | Description | UniProt  
A | E3 ubiquitin-protein ligase RNF38 | RNF38_HUMAN  
B | Ubiquitin-conjugating enzyme E2 K | UBE2K_HUMAN  
C | Polyubiquitin-B | UBB_HUMAN  
D | Polyubiquitin-B | UBB_HUMAN  
E | Polyubiquitin-B | UBB_HUMAN  
  
Non-standard residues in 7ojx #15  
---  
ME7 — 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)  
ZN — zinc ion  
  

> matchmaker #!15 to #14/A pairing bs

Parameters  
---  
Chain pairing | bs  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker full-model-7.pdb, chain A (#14) with 7ojx, chain B (#15), sequence
alignment score = 298.9  
RMSD between 112 pruned atom pairs is 0.940 angstroms; (across all 157 pairs:
7.065)  
  

> select add #15

3731 atoms, 3746 bonds, 9 pseudobonds, 541 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select clear

> select #15/A

529 atoms, 534 bonds, 8 pseudobonds, 75 residues, 2 models selected  

> delete sel

> hide #!14 models

> show #!14 models

> hide #!15 models

> select clear

> ui mousemode right select

> select clear

> select #14/A:93

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

> show sel atoms

> hide sel atoms

> show sel atoms

> style sel stick

Changed 6 atom styles  

> color sel lime

> select clear

Drag select of 16 residues  

> select clear

> select #14/A:138

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

> style sel stick

Changed 6 atom styles  

> show sel atoms

> color sel forest green

> select clear

> show #!15 models

> ui mousemode right translate

> ui mousemode right select

> select #15/D:47

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

> select #15/D:48

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

> show sel atoms

> show sel cartoons

> style sel stick

Changed 6 atom styles  

> color sel forest green

> select clear

Drag select of 2 residues  

> select clear

> select #15/B

1562 atoms, 1566 bonds, 1 pseudobond, 228 residues, 2 models selected  

> delete sel

> ui mousemode right translate

> select #15/C

561 atoms, 564 bonds, 79 residues, 1 model selected  

> delete sel

> save /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_29.cxs includeMaps
> true

> select ::name="PO4"

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

> select add #11

5302 atoms, 5029 bonds, 590 residues, 1 model selected  

> select subtract #11

Nothing selected  

> select ::name="U94"

49 atoms, 50 bonds, 1 residue, 1 model selected  

> select add #11

5302 atoms, 5029 bonds, 590 residues, 1 model selected  

> select subtract #11

Nothing selected  

> select ::name="EDO"

30 atoms, 27 bonds, 3 residues, 1 model selected  

> select add #11

5302 atoms, 5029 bonds, 590 residues, 1 model selected  

> select subtract #11

Nothing selected  

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J412_002_volume_map_sharp.mrc

Opened cryosparc_P9_J412_002_volume_map_sharp.mrc as #16, grid size
144,144,144, pixel 2.47, shown at level 0.0775, step 1, values float32  

> volume flip #16

Opened cryosparc_P9_J412_002_volume_map_sharp.mrc z flip as #17, grid size
144,144,144, pixel 2.47, shown at step 1, values float32  

> volume #17 level 0.1448

> select add #17

2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.9922,0.0044226,0.12458,-22.95,1.9255e-05,0.99937,-0.03563,6.8457,-0.12466,0.035355,0.99157,17.52

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.9922,0.0044226,0.12458,-22.362,1.9255e-05,0.99937,-0.03563,11.357,-0.12466,0.035355,0.99157,10.34

> view matrix models
> #17,0.9922,0.0044226,0.12458,-22.105,1.9255e-05,0.99937,-0.03563,16.904,-0.12466,0.035355,0.99157,11.29

> ui mousemode right "rotate selected models"

> view matrix models
> #17,0.71959,0.6866,0.10379,-85.778,-0.69179,0.72177,0.021512,174.71,-0.060147,-0.087284,0.99437,20.189

> ui mousemode right "translate selected models"

> view matrix models
> #17,0.71959,0.6866,0.10379,-85.787,-0.69179,0.72177,0.021512,174.94,-0.060147,-0.087284,0.99437,24.387

> select clear

> hide #!13 models

> hide #!13.1 models

> hide #!14 models

> show #!14 models

> hide #!17 models

> select add #14

21476 atoms, 21738 bonds, 13 pseudobonds, 1524 residues, 3 models selected  

> select add #15

22555 atoms, 22818 bonds, 13 pseudobonds, 1683 residues, 4 models selected  

> combine sel

Remapping chain ID 'D' in 7ojx #15 to 'G'  
Remapping chain ID 'E' in 7ojx #15 to 'H'  

> show #!17 models

> hide #!14 models

> hide #!15 models

> select subtract #14

1079 atoms, 1080 bonds, 159 residues, 1 model selected  

> select subtract #15

Nothing selected  

> fitmap #18 inMap #17

Fit molecule combination (#18) to map
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) using 22555 atoms  
average map value = 0.447, steps = 112  
shifted from previous position = 9.21  
rotated from previous position = 19.6 degrees  
atoms outside contour = 3053, contour level = 0.14484  
  
Position of combination (#18) relative to
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates:  
Matrix rotation and translation  
-0.97806640 -0.06230326 -0.19875723 422.48504677  
0.06581407 -0.99777016 -0.01109996 366.20147167  
-0.19762247 -0.02393752 0.97998590 23.12448917  
Axis -0.09969844 -0.00881272 0.99497867  
Axis point 206.47417814 190.00859521 0.00000000  
Rotation angle (degrees) 176.30863292  
Shift along axis -22.33995844  
  

> select clear

> surface dust #17 size 24.7

> volume #17 level 0.2526

> volume #17 level 0.1448

> volume #17 level 0.1493

> volume #17 level 0.1987

> volume #17 level 0.1269

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P9_J649_006_volume_map_sharp.mrc

Opened cryosparc_P9_J649_006_volume_map_sharp.mrc as #19, grid size
420,420,420, pixel 0.825, shown at level 0.0268, step 2, values float32  

> volume #19 level 0.05665

> volume flip #19

Opened cryosparc_P9_J649_006_volume_map_sharp.mrc z flip as #20, grid size
420,420,420, pixel 0.825, shown at step 1, values float32  

> fitmap #20 inMap #17

Fit map cryosparc_P9_J649_006_volume_map_sharp.mrc z flip in map
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 287605 points  
correlation = 0.9078, correlation about mean = 0.6488, overlap = 2.095e+04  
steps = 188, shift = 14, angle = 44 degrees  
  
Position of cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#20) relative
to cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates:  
Matrix rotation and translation  
0.99999751 -0.00223074 -0.00003978 5.13478599  
0.00223068 0.99999658 -0.00136232 4.84445548  
0.00004281 0.00136223 0.99999907 3.01854380  
Axis 0.52112337 -0.01579715 0.85333515  
Axis point -2206.70833640 1095.32414338 0.00000000  
Rotation angle (degrees) 0.14977758  
Shift along axis 5.17515790  
  

> surface dust #17 size 24.7

> surface dust #20 size 8.25

> open
> /home/pinkie/Documents/Charlotte/2024_01_28/cryosparc_P14_J581_003_volume_map_sharp.mrc

Opened cryosparc_P14_J581_003_volume_map_sharp.mrc as #21, grid size
128,128,128, pixel 3.38, shown at level 0.0872, step 1, values float32  

> surface dust #21 size 33.8

> volume #21 level 0.3273

> fitmap #21 inMap #17

Fit map cryosparc_P14_J581_003_volume_map_sharp.mrc in map
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 6517 points  
correlation = 0.4039, correlation about mean = -0.01045, overlap = 553.7  
steps = 436, shift = 15.8, angle = 37.9 degrees  
  
Position of cryosparc_P14_J581_003_volume_map_sharp.mrc (#21) relative to
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates:  
Matrix rotation and translation  
0.98601219 -0.14446284 -0.08312907 19.61215113  
0.11673704 0.95455998 -0.27420378 36.87216779  
0.11896395 0.26066403 0.95807194 -57.49708785  
Axis 0.85087384 -0.32149189 0.41551976  
Axis point 0.00000000 202.82855623 78.51350943  
Rotation angle (degrees) 18.31886274  
Shift along axis -19.05781241  
  

> select add #21

4 models selected  

> ui mousemode right "translate selected models"

> view matrix models
> #21,0.80202,0.57851,-0.14864,-91.371,-0.5953,0.79452,-0.1198,180.05,0.048799,0.18457,0.98161,-96.697

> ui mousemode right "rotate selected models"

> view matrix models
> #21,0.80229,0.52541,0.28334,-180.65,-0.57975,0.7989,0.16015,110.76,-0.14221,-0.29275,0.94555,52.725

> volume flip #21

Opened cryosparc_P14_J581_003_volume_map_sharp.mrc z flip as #22, grid size
128,128,128, pixel 3.38, shown at step 1, values float32  

> fitmap #22 inMap #17

Fit map cryosparc_P14_J581_003_volume_map_sharp.mrc z flip in map
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 6517 points  
correlation = 0.6482, correlation about mean = 0.2156, overlap = 1441  
steps = 164, shift = 21.6, angle = 36.5 degrees  
  
Position of cryosparc_P14_J581_003_volume_map_sharp.mrc z flip (#22) relative
to cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates:  
Matrix rotation and translation  
0.93922058 0.34326503 -0.00581154 -100.97458873  
-0.33951902 0.92619472 -0.16398211 87.22555980  
-0.05090671 0.15598850 0.98644617 -55.53042614  
Axis 0.42358526 0.05969814 -0.90388697  
Axis point 180.41192944 341.68760540 0.00000000  
Rotation angle (degrees) 22.19087245  
Shift along axis 12.62908512  
  

> select add #22

4 models selected  

> select subtract #21

2 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #22,-0.55164,0.82005,0.15235,94.206,0.83403,0.54034,0.11145,-132.93,0.0090744,0.18855,-0.98202,315.23

> ui mousemode right "translate selected models"

> view matrix models
> #22,-0.55164,0.82005,0.15235,95.398,0.83403,0.54034,0.11145,-131.11,0.0090744,0.18855,-0.98202,328.09

> fitmap #22 inMap #17

Fit map cryosparc_P14_J581_003_volume_map_sharp.mrc z flip in map
cryosparc_P9_J412_002_volume_map_sharp.mrc z flip using 6517 points  
correlation = 0.9521, correlation about mean = 0.7986, overlap = 2739  
steps = 168, shift = 10.8, angle = 18.3 degrees  
  
Position of cryosparc_P14_J581_003_volume_map_sharp.mrc z flip (#22) relative
to cryosparc_P9_J412_002_volume_map_sharp.mrc z flip (#17) coordinates:  
Matrix rotation and translation  
-0.99979594 0.02007438 -0.00224759 390.44908315  
0.01996422 0.99894363 0.04138837 -50.61062770  
0.00307606 0.04133505 -0.99914059 376.77240244  
Axis -0.01001209 -0.99973588 -0.02068651  
Axis point 195.22657357 0.00000000 189.17004184  
Rotation angle (degrees) 179.84744828  
Shift along axis 38.89394229  
  

> select clear

> volume #22 level 0.1832

> volume #22 level 0.2252

> volume #22 level 0.2552

> select #18/H

478 atoms, 481 bonds, 74 residues, 1 model selected  

> delete sel

> show #!19 models

> show #!20 models

> hide #!19 models

> volume #19 level 0.1077

> volume #20 level 0.08004

> volume #19 level 0.09923

> volume #20 level 0.07069

> hide #!18 models

> show #!18 models

> hide #!20 models

> save /home/pinkie/Documents/Charlotte/2024_01_28/with-Ubacceptor.pdb models
> #18

> select #18/G

601 atoms, 598 bonds, 85 residues, 1 model selected  

> delete sel

> save /home/pinkie/Documents/Charlotte/2024_01_28/without-Ubacceptor.pdb

> show #!22 models

> hide #!22 models

> show #!22 models

> hide #!22 models

> select #18/B

2615 atoms, 2648 bonds, 160 residues, 1 model selected  

> color sel forest green

> select clear

> select #18/C

1647 atoms, 1663 bonds, 104 residues, 1 model selected  

> color sel #ccce3fff

> select #18/D

1522 atoms, 1539 bonds, 97 residues, 1 model selected  

> color sel #b0daa8ff

> select #18/E

10756 atoms, 10867 bonds, 658 residues, 1 model selected  

> color sel #4293a5ff

> select #18/F

1835 atoms, 1858 bonds, 114 residues, 1 model selected  

> color sel #5b42cdff

> select #18/N

605 atoms, 610 bonds, 77 residues, 1 model selected  

> color sel cyan

> select clear

> select #18/R

499 atoms, 508 bonds, 13 pseudobonds, 63 residues, 3 models selected  

> color (#!18 & sel) #60cb3eff

> select #18/A

1422 atoms, 1464 bonds, 176 residues, 1 model selected  

> color sel #e01b24ff

> color sel #c01c28ff

> select clear

> ui mousemode right select

> select clear

[Repeated 2 time(s)]

> color sel orange

> select clear

Drag select of 2 atoms, 2 bonds  

> color sel orange

> select clear

[Repeated 1 time(s)]

> ui mousemode right select

Drag select of 1 atoms, 1 residues  

> color sel magenta

> select clear

> select sequence GELPER

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #18/A

Alignment identifier is 18/A  

> select #18/A:107

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

> select #18/A:107-119

107 atoms, 110 bonds, 13 residues, 1 model selected  

> select #18/A:102

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

> select #18/A:102-113

92 atoms, 93 bonds, 12 residues, 1 model selected  

> color sel gray

> select clear

Drag select of 3 residues  

> select clear

> ui mousemode right translate

> select #18/A:98

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

> select #18/A:98-99

17 atoms, 18 bonds, 2 residues, 1 model selected  

> select #18/A:91

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

> select #18/A:91-102

90 atoms, 92 bonds, 12 residues, 1 model selected  

> select clear

> select #18/A:91-102

90 atoms, 92 bonds, 12 residues, 1 model selected  

> select clear

> ui mousemode right select

> select #18/A:91-102

90 atoms, 92 bonds, 12 residues, 1 model selected  

> select clear

> select #18/A:96

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

> select #18/A:97

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

> select #18/A:96

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

> select #18/A:97

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

> select #18/A:99

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

> select #18/A:101

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

> select clear

[Repeated 1 time(s)]

> ui mousemode right select

> select #18/A:8-22,95-97,120-132,142-153,160-176

478 atoms, 477 bonds, 60 residues, 1 model selected  

> select #18/A:91-92

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

> select #18/A:91-118

219 atoms, 226 bonds, 28 residues, 1 model selected  

> select #18/A:91

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

> select #18/A:91-94

29 atoms, 28 bonds, 4 residues, 1 model selected  

> select #18/A:98

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

> select #18/A:98-104

54 atoms, 57 bonds, 7 residues, 1 model selected  

> select #18/A:95

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

> select #18/A:95-105

85 atoms, 88 bonds, 11 residues, 1 model selected  

> color sel gray

> select #18/A:107

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

> select #18/A:107-119

107 atoms, 110 bonds, 13 residues, 1 model selected  

> color sel gray

> select clear

> ui mousemode right translate

> save
> /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_29_chimeramodelling.cxs
> includeMaps true

> ui mousemode right select

> select #18/F:456

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

> show sel atoms

> style sel stick

Changed 22 atom styles  

> color sel hot pink

> select clear

[Repeated 2 time(s)]

> save
> /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_30_chimerasession.cxs
> includeMaps true

> close #4

> close #13

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!17 models

> hide #!17 models

> close #16

> show #!19 models

> hide #!19 models

> show #!20 models

> hide #!20 models

> close #19

> show #!21 models

> hide #!21 models

> show #!22 models

> hide #!22 models

> close #21

> hide #!18 models

> show #!18 models

> show #!1 models

> hide #!1 models

> show #!1 models

> close #1

> show #!2.1 models

> hide #!2.1 models

> show #!2.4 models

> hide #!2.4 models

> close #2

> show #3 models

> hide #3 models

> show #3 models

> hide #3 models

> close #3

> show #!5 models

> hide #!5 models

> show #!5 models

> hide #!5 models

> close #5

> show #!6 models

> hide #!6 models

> close #6

> close #7

> show #!8 models

> hide #!8 models

> close #8

> show #9 models

> hide #9 models

> close #9

> show #!10 models

> hide #!10 models

> close #10

> show #11 models

> hide #11 models

> show #!12 models

Drag select of 60 residues  

> ui mousemode right translate

> select clear

> show #!14 models

> hide #!12 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!15 models

> hide #!15 models

> show #!15 models

> hide #!15 models

> show #!17 models

> hide #!17 models

> show #!20 models

> hide #!18 models

> show #!17 models

> transparency #17.1#20.1 50

> show #!18 models

> volume #17 level 0.1533

> show #!15 models

> hide #!15 models

> hide #!17 models

> show #!17 models

> show #!22 models

> hide #!22 models

> save
> /home/pinkie/Documents/Charlotte/2024_01_28/2024_01_30_v2_chimerasession.cxs
> includeMaps true

——— End of log from Tue Jan 30 11:29:44 2024 ———

opened ChimeraX session  

> hide #!18 models

> hide #!20 models

> show #!20 models

> hide #!17 models

> show #!17 models

> show #!14 models

> show #!12 models

> show #11 models

> hide #11 models

> hide #!12 models

> hide #!14 models

> show #!22 models

> hide #!22 models

> show #!22 models

> show #!18 models

> hide #!18 models

> show #!18 models

> lighting soft

> transparency 0

> transparency 50

> volume #22 level 0.3822

> volume #22 level 0.2552

> volume #22 level 0.4046

> hide #!22 models

> show #!14 models

> hide #!14 models

> show #!14 models

> hide #!14 models

> show #!12 models

> hide #!12 models

> show #!12 models

> hide #!12 models

> hide #!18 models

> show #!18 models

> open
> /home/pinkie/Documents/Charlotte/2024_06/cryosparc_P9_J659_007_volume_map_sharp.mrc
> /home/pinkie/Documents/Charlotte/2024_06/cryosparc_P9_J659_007_volume_map.mrc

Opened cryosparc_P9_J659_007_volume_map_sharp.mrc as #1.1, grid size
480,480,480, pixel 0.825, shown at level 0.0225, step 2, values float32  
Opened cryosparc_P9_J659_007_volume_map.mrc as #1.2, grid size 480,480,480,
pixel 0.825, shown at level 0.00707, step 2, values float32  

> hide #!18 models

> volume #1.2 level 0.01906

> volume #1.1 level 0.05696

> select add #1.1

4 models selected  

> select add #1.2

8 models selected  

> ui mousemode right "translate selected models"

> ui mousemode right "rotate selected models"

> view matrix models
> #1.1,-0.73945,-0.66601,-0.098215,503.62,0.63499,-0.73846,0.22688,164.46,-0.22363,0.1054,0.96896,31.101,#1.2,-0.73945,-0.66601,-0.098215,503.62,0.63499,-0.73846,0.22688,164.46,-0.22363,0.1054,0.96896,31.101

> ui mousemode right "translate selected models"

> view matrix models
> #1.1,-0.73945,-0.66601,-0.098215,500.05,0.63499,-0.73846,0.22688,152.07,-0.22363,0.1054,0.96896,5.6966,#1.2,-0.73945,-0.66601,-0.098215,500.05,0.63499,-0.73846,0.22688,152.07,-0.22363,0.1054,0.96896,5.6966

> view matrix models
> #1.1,-0.73945,-0.66601,-0.098215,476.35,0.63499,-0.73846,0.22688,165.36,-0.22363,0.1054,0.96896,2.2825,#1.2,-0.73945,-0.66601,-0.098215,476.35,0.63499,-0.73846,0.22688,165.36,-0.22363,0.1054,0.96896,2.2825

> fitmap #1.1 inMap #20

Fit map cryosparc_P9_J659_007_volume_map_sharp.mrc in map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip using 36781 points  
correlation = 0.9171, correlation about mean = 0.7903, overlap = 799.1  
steps = 252, shift = 7.76, angle = 15 degrees  
  
Position of cryosparc_P9_J659_007_volume_map_sharp.mrc (#1.1) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#20) coordinates:  
Matrix rotation and translation  
-0.99948342 0.01340843 -0.02920822 373.96402547  
-0.01366728 -0.99986892 0.00868053 372.14706467  
-0.02908800 0.00907524 0.99953566 -21.05899600  
Axis 0.01457641 -0.00443965 -0.99988390  
Axis point 188.08875457 184.85549199 0.00000000  
Rotation angle (degrees) 179.22422433  
Shift along axis 24.85540421  
  

> fitmap #1.2 inMap #20

Fit map cryosparc_P9_J659_007_volume_map.mrc in map
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip using 78730 points  
correlation = 0.8962, correlation about mean = 0.818, overlap = 608.1  
steps = 240, shift = 9.04, angle = 15.1 degrees  
  
Position of cryosparc_P9_J659_007_volume_map.mrc (#1.2) relative to
cryosparc_P9_J649_006_volume_map_sharp.mrc z flip (#20) coordinates:  
Matrix rotation and translation  
-0.99955306 0.01397128 -0.02642920 373.41485214  
-0.01420867 -0.99986019 0.00881572 372.23852295  
-0.02630234 0.00918730 0.99961182 -21.62260651  
Axis 0.01318482 -0.00450140 -0.99990294  
Axis point 187.87678898 184.85341547 0.00000000  
Rotation angle (degrees) 179.19259892  
Shift along axis 24.86831902  
  

> select subtract #1.2

4 models selected  

> select subtract #1.1

Nothing selected  

> hide #!20 models

> show #!20 models

> hide #!20 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> show #!1.2 models

> show #!18 models

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> surface dust #1.1 size 8.25

> show #!1.2 models

> volume #1.2 step 1

> volume #1.1 step 1

> transparency #1.1.1 50

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
note | Fetching compressed mmCIF 8rx0 from
http://files.rcsb.org/download/8rx0.cif  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #2  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #2  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

> hide #!18 models

> select add #2

21370 atoms, 21642 bonds, 13 pseudobonds, 1548 residues, 3 models selected  

> fitmap #2 inMap #1.1

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map_sharp.mrc
(#1.1) using 21370 atoms  
average map value = 0.1073, steps = 68  
shifted from previous position = 0.808  
rotated from previous position = 1.01 degrees  
atoms outside contour = 8594, contour level = 0.056956  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map_sharp.mrc
(#1.1) coordinates:  
Matrix rotation and translation  
-0.73092142 0.68081307 0.04740703 197.96935832  
-0.67616473 -0.73184263 0.08489771 441.44230993  
0.09249396 0.02999859 0.99526124 3.71445652  
Axis -0.04040157 -0.03318055 -0.99863245  
Axis point 185.35205193 182.02538297 0.00000000  
Rotation angle (degrees) 137.20181648  
Shift along axis -26.35494835  
  

> select clear

> style #!2 stick

Changed 21370 atom styles  

> show #!2 cartoons

> volume #1.1 level 0.1472

> view

> show #!2 atoms

> select ::name="759"

69 atoms, 75 bonds, 1 residue, 1 model selected  

> color sel yellow

> select clear

> volume #1.1 level 0.1021

> hide #!2 models

> transparency #1.1.1 0

> show #!1.2 models

> volume #1.2 level 0.1935

> volume #1.2 level 0.02577

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> volume #1.2 level 0.05149

> volume #1.2 level 0.03919

> volume #1.2 level 0.1141

> show #!2 models

> transparency #1.2.1 50

> select sidechain only

Expected a keyword  

> select sidechain

69673 atoms, 64004 bonds, 6516 residues, 6 models selected  

> select solvent

976 atoms, 638 bonds, 338 residues, 3 models selected  

> delete sel

> select #2/A:sidechain

Nothing selected  

> select #2/A sidechain

Expected a keyword  

> select #2/A sidechain

Expected a keyword  

> select #2 sidechain

Expected a keyword  

> select sidechain

69673 atoms, 64004 bonds, 6516 residues, 6 models selected  

> select sidechain #2

Expected a keyword  

> select sidechain

69673 atoms, 64004 bonds, 6516 residues, 6 models selected  

> select #2

21362 atoms, 21642 bonds, 13 pseudobonds, 1540 residues, 3 models selected  

> select #2/A

885 atoms, 908 bonds, 111 residues, 1 model selected  

> select #2/Asidechain

Nothing selected  

> select #2/A sidechain

Expected a keyword  

> select #2/A sidechains

Expected a keyword  

> select #2/A sidechain

Expected a keyword  

> select #2/A-sidechain

20787 atoms, 21061 bonds, 13 pseudobonds, 1465 residues, 3 models selected  

> select #2/A sidechain

Expected a keyword  

> select #2/A@sidechain

Nothing selected  

> select #2/A:Ca

Nothing selected  

> select Ca

Nothing selected  

> select @Ca

6517 atoms, 6517 residues, 6 models selected  

> select @sidechain

Nothing selected  

> select @Cb

6225 atoms, 6225 residues, 6 models selected  

> select

94351 atoms, 95475 bonds, 52 pseudobonds, 6534 residues, 25 models selected  

> select #2/A@Ca

111 atoms, 111 residues, 1 model selected  

> hide sel atoms

> show sel atoms

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> show sel cartoons

> select #2/A@Ca

111 atoms, 111 residues, 1 model selected  

> view matrix models
> #2,0.99998,-0.0028888,-0.0047606,2.4594,0.0029684,0.99985,0.016795,-1.2113,0.0047114,-0.016809,0.99985,-2.2479

> undo

> select clear

> select #2/A sideonly

Expected a keyword  

> select #2/A :sideonly

Nothing selected  

> select #2/A :sidechain

Nothing selected  

> select #2/A & sidechain

552 atoms, 459 bonds, 111 residues, 1 model selected  

> select #2/A & sideonly

441 atoms, 351 bonds, 108 residues, 1 model selected  

> hide sel cartoons

> select #2/A & sidechain

552 atoms, 459 bonds, 111 residues, 1 model selected  

> select #2/A & sideonly

441 atoms, 351 bonds, 108 residues, 1 model selected  

> select #2/A & sidechain

552 atoms, 459 bonds, 111 residues, 1 model selected  

> delete sel

Undo failed, probably because structures have been modified.  

> show #!2 cartoons

[Repeated 1 time(s)]

> hide #!2 atoms

[Repeated 1 time(s)]

> show #!2 cartoons

> hide #!2 surfaces

> hide #!2 cartoons

> show #!2 cartoons

> show #!2 atoms

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #3  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #3  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

> show #!2-3 cartoons

> hide #!2-3 atoms

> hide #!2-3 surfaces

> close #2

> select add #3

21370 atoms, 21642 bonds, 13 pseudobonds, 1548 residues, 3 models selected  

> fitmap #3 inMap #1.2

Fit molecule 8rx0 (#3) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
using 21370 atoms  
average map value = 0.09099, steps = 80  
shifted from previous position = 0.965  
rotated from previous position = 0.797 degrees  
atoms outside contour = 14570, contour level = 0.1141  
  
Position of 8rx0 (#3) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
-0.73601744 0.67550999 0.04432354 200.70850250  
-0.67100751 -0.73664288 0.08429815 441.51062032  
0.08959486 0.03230348 0.99545428 3.91215108  
Axis -0.03856367 -0.03357706 -0.99869186  
Axis point 185.81581942 181.92454516 0.00000000  
Rotation angle (degrees) 137.61254970  
Shift along axis -26.47171863  
  

> select clear

> select #2/A & sidechain

Nothing selected  

> show #!3 atoms

> style #!3 stick

Changed 21370 atom styles  

> select #2/A & sidechain

Nothing selected  

> select #3/A & sidechain

552 atoms, 459 bonds, 111 residues, 1 model selected  

> hide sel

> remove sel

Unknown command: remove sel  

> hide sel

> color bfactor sel

552 atoms, 111 residues, atom bfactor range 38.1 to 137  

> select clear

> show #!3 atoms

> select #3/A:349-350 & sidechain

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

> delete sel

> select #3/A & sidechain

546 atoms, 455 bonds, 109 residues, 1 model selected  

> delete sel

> show #!3 atoms

> hide #!3 atoms

> show #!3 atoms

> hide #!3 atoms

> show #!3 atoms

> ui mousemode right select

Drag select of 3 residues  

> delete sel

Undo failed, probably because structures have been modified.  

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #2  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #2  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

> close #3

> fitmap #2 inMap #1.2

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
using 21370 atoms  
average map value = 0.09099, steps = 80  
shifted from previous position = 0.965  
rotated from previous position = 0.797 degrees  
atoms outside contour = 14570, contour level = 0.1141  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
-0.73601744 0.67550999 0.04432354 200.70850250  
-0.67100751 -0.73664288 0.08429815 441.51062032  
0.08959486 0.03230348 0.99545428 3.91215108  
Axis -0.03856367 -0.03357706 -0.99869186  
Axis point 185.81581942 181.92454516 0.00000000  
Rotation angle (degrees) 137.61254970  
Shift along axis -26.47171863  
  

> show #!2 cartoons

> hide #!2 atoms

> show #!2 atoms

> style #!2 stick

Changed 21370 atom styles  

> color bfactor #!2

21370 atoms, 1548 residues, atom bfactor range 29 to 137  

> select clear

> ui mousemode right translate

> select #2/A & sidechain

552 atoms, 459 bonds, 111 residues, 1 model selected  

> delete sel

> select clear

> select #2/A:457-459

9 atoms, 5 bonds, 3 residues, 1 model selected  

> delete sel

> show #!2 cartoons

> hide #!2 cartoons

> show #!2 cartoons

> hide #!2 cartoons

> show #!2 cartoons

> hide #!2 atoms

> show #!2 atoms

> close #2

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #2  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #2  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

> fitmap #2 inMap #1.2

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
using 21370 atoms  
average map value = 0.09099, steps = 80  
shifted from previous position = 0.965  
rotated from previous position = 0.797 degrees  
atoms outside contour = 14570, contour level = 0.1141  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
-0.73601744 0.67550999 0.04432354 200.70850250  
-0.67100751 -0.73664288 0.08429815 441.51062032  
0.08959486 0.03230348 0.99545428 3.91215108  
Axis -0.03856367 -0.03357706 -0.99869186  
Axis point 185.81581942 181.92454516 0.00000000  
Rotation angle (degrees) 137.61254970  
Shift along axis -26.47171863  
  

> fitmap #2 inMap #1.2

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
using 21370 atoms  
average map value = 0.09099, steps = 64  
shifted from previous position = 0.0123  
rotated from previous position = 0.00696 degrees  
atoms outside contour = 14571, contour level = 0.1141  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
-0.73598978 0.67553655 0.04437792 200.68940166  
-0.67102310 -0.73661694 0.08440070 441.48695869  
0.08970529 0.03233944 0.99544317 3.87523220  
Axis -0.03861172 -0.03361746 -0.99868864  
Axis point 185.80643210 181.91519277 0.00000000  
Rotation angle (degrees) 137.61074426  
Shift along axis -26.46078590  
  

> hide #!2 atoms

> show #!2 atoms

> style #!2 stick

Changed 21370 atom styles  

> show #!2 cartoons

> select #2/A:457-459

23 atoms, 23 bonds, 3 residues, 1 model selected  

> delete sel

> select #2/A & sidechain

538 atoms, 448 bonds, 108 residues, 1 model selected  

> delete sel

> select #2/A:349-350

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

> delete sel

> close #2

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #2  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #2  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

> fitmap #2 inMap #1.2

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map.mrc (#1.2)
using 21370 atoms  
average map value = 0.09099, steps = 80  
shifted from previous position = 0.965  
rotated from previous position = 0.797 degrees  
atoms outside contour = 14570, contour level = 0.1141  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map.mrc (#1.2)
coordinates:  
Matrix rotation and translation  
-0.73601744 0.67550999 0.04432354 200.70850250  
-0.67100751 -0.73664288 0.08429815 441.51062032  
0.08959486 0.03230348 0.99545428 3.91215108  
Axis -0.03856367 -0.03357706 -0.99869186  
Axis point 185.81581942 181.92454516 0.00000000  
Rotation angle (degrees) 137.61254970  
Shift along axis -26.47171863  
  

> hide #!2 atoms

> style #!2 stick

Changed 21370 atom styles  

> show #!2 atoms

> show #!2 cartoons

> volume #1.2 level 0.07162

> volume #1.2 level 0.09621

> volume #1.1 level 0.09081

> volume #1.1 level 0.07953

> select #2/A:456

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

> select #2/G:138

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

> select #2/G:93

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

> select #2/A & sidechain

552 atoms, 459 bonds, 111 residues, 1 model selected  

> delete sel

> color bfactor #!2

20818 atoms, 1548 residues, atom bfactor range 29 to 124  

> select #2/N & sidechain

374 atoms, 300 bonds, 77 residues, 1 model selected  

> delete sel

> volume #1.1 level 0.1171

> volume #1.1 level 0.08329

Drag select of 4 residues  

> delete sel

> close #2

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #2  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #2  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps,
got 1 atomic models, 0 maps.  

> hide #!1 models

> show #!1.1 models

> fitmap #2 inMap #1.1

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map_sharp.mrc
(#1.1) using 21370 atoms  
average map value = 0.1073, steps = 68  
shifted from previous position = 0.808  
rotated from previous position = 1.01 degrees  
atoms outside contour = 11206, contour level = 0.08329  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map_sharp.mrc
(#1.1) coordinates:  
Matrix rotation and translation  
-0.73092142 0.68081307 0.04740703 197.96935832  
-0.67616473 -0.73184263 0.08489771 441.44230993  
0.09249396 0.02999859 0.99526124 3.71445652  
Axis -0.04040157 -0.03318055 -0.99863245  
Axis point 185.35205193 182.02538297 0.00000000  
Rotation angle (degrees) 137.20181648  
Shift along axis -26.35494835  
  

> select clear

> hide #!2 atoms

> show #!2 atoms

> style #!2 stick

Changed 21370 atom styles  

> show #!2 cartoons

> color bfactor #!2

21370 atoms, 1548 residues, atom bfactor range 29 to 137  
Drag select of 9 atoms, 4 residues, 7 bonds  

> select clear

Drag select of 4 atoms, 3 residues, 2 bonds  

> delete sel

Drag select of 10 atoms, 3 residues, 9 bonds  

> delete sel

Drag select of 10 atoms, 4 residues, 8 bonds  

> delete sel

> select #2/A:406

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

> select #2/A:407

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

> select #2/A:405

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

> select #2/A:405-412

35 atoms, 34 bonds, 1 pseudobond, 4 residues, 2 models selected  

> delete sel

> select #2/A & sidechain

484 atoms, 404 bonds, 97 residues, 1 model selected  

> delete sel

> select #2/N & sidechain

374 atoms, 300 bonds, 77 residues, 1 model selected  

> delete sel

> volume #1.1 level 0.07953

> volume #1.1 level 0.1247

> volume #1.1 level 0.2639

> save /home/pinkie/Documents/Charlotte/2024_06/done-brd4-n8.cxs includeMaps
> true

——— End of log from Wed Jun 26 10:54:46 2024 ———

opened ChimeraX session  

> split chains

Split 6nyo (#11) into 2 models  
Split full-model-9-isoldeatt1.pdb (#12) into 9 models  
Split full-model-7.pdb (#14) into 9 models  
Split 7ojx (#15) into 2 models  
Split combination (#18) into 9 models  
Split 8rx0 (#2) into 9 models  
Chain information for 6nyo A #11.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 6nyo E #11.2  
---  
Chain | Description  
E | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb A #12.1  
---  
Chain | Description  
A | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb B #12.2  
---  
Chain | Description  
B | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb C #12.3  
---  
Chain | Description  
C | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb D #12.4  
---  
Chain | Description  
D | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb E #12.5  
---  
Chain | Description  
E | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb F #12.6  
---  
Chain | Description  
F | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb N #12.7  
---  
Chain | Description  
N | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb R #12.8  
---  
Chain | Description  
R | No description available  
  
Chain information for full-model-9-isoldeatt1.pdb U #12.9  
---  
Chain | Description  
U | No description available  
  
Chain information for full-model-7.pdb A #14.1  
---  
Chain | Description  
A | No description available  
  
Chain information for full-model-7.pdb B #14.2  
---  
Chain | Description  
B | No description available  
  
Chain information for full-model-7.pdb C #14.3  
---  
Chain | Description  
C | No description available  
  
Chain information for full-model-7.pdb D #14.4  
---  
Chain | Description  
D | No description available  
  
Chain information for full-model-7.pdb E #14.5  
---  
Chain | Description  
E | No description available  
  
Chain information for full-model-7.pdb F #14.6  
---  
Chain | Description  
F | No description available  
  
Chain information for full-model-7.pdb N #14.7  
---  
Chain | Description  
N | No description available  
  
Chain information for full-model-7.pdb R #14.8  
---  
Chain | Description  
R | No description available  
  
Chain information for full-model-7.pdb U #14.9  
---  
Chain | Description  
U | No description available  
  
Chain information for 7ojx D #15.1  
---  
Chain | Description  
D | No description available  
  
Chain information for 7ojx E #15.2  
---  
Chain | Description  
E | No description available  
  
Chain information for combination A #18.1  
---  
Chain | Description  
A | No description available  
  
Chain information for combination B #18.2  
---  
Chain | Description  
B | No description available  
  
Chain information for combination C #18.3  
---  
Chain | Description  
C | No description available  
  
Chain information for combination D #18.4  
---  
Chain | Description  
D | No description available  
  
Chain information for combination E #18.5  
---  
Chain | Description  
E | No description available  
  
Chain information for combination F #18.6  
---  
Chain | Description  
F | No description available  
  
Chain information for combination N #18.7  
---  
Chain | Description  
N | No description available  
  
Chain information for combination R #18.8  
---  
Chain | Description  
R | No description available  
  
Chain information for combination U #18.9  
---  
Chain | Description  
U | No description available  
  
Chain information for 8rx0 A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for 8rx0 B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for 8rx0 C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for 8rx0 D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for 8rx0 E #2.5  
---  
Chain | Description  
E | No description available  
  
Chain information for 8rx0 G #2.6  
---  
Chain | Description  
G | No description available  
  
Chain information for 8rx0 N #2.7  
---  
Chain | Description  
N | No description available  
  
Chain information for 8rx0 R #2.8  
---  
Chain | Description  
R | No description available  
  
Chain information for 8rx0 U #2.9  
---  
Chain | Description  
U | No description available  
  

> hide #!2.1 models

> show #!2.1 models

> show #2.2-7,9#!2.1,8 cartoons

> hide #2.2-7,9#!2.1,8 cartoons

> show #2.2-7,9#!2.1,8 cartoons

> hide #2.2-7,9#!2.1,8 cartoons

> hide #2.2-7,9#!2.1,8 atoms

> show #2.2-7,9#!2.1,8 atoms

> hide #2.2-7,9#!2.1,8 cartoons

> show #2.2-7,9#!2.1,8 cartoons

> show #2.2-7,9#!2.1,8 surfaces

> hide #!2.1-9 surfaces

> show #!2.1-9 cartoons

> rainbow #!2.1-9

> mlp #!2.1-9

Map values for surface "8rx0 A_A SES surface": minimum -24.87, mean -14.54,
maximum -1.371  
Map values for surface "8rx0 B_B SES surface": minimum -24.78, mean -2.806,
maximum 23.67  
Map values for surface "8rx0 C_C SES surface": minimum -25.1, mean -4.285,
maximum 24.52  
Map values for surface "8rx0 D_D SES surface": minimum -27.3, mean -2.396,
maximum 26.24  
Map values for surface "8rx0 E_E SES surface": minimum -27.38, mean -3.428,
maximum 25.11  
Map values for surface "8rx0 G_G SES surface": minimum -28.53, mean -4.035,
maximum 23.01  
Map values for surface "8rx0 N_N SES surface": minimum -25.81, mean -14.73,
maximum -1.589  
Map values for surface "8rx0 U_U SES surface": minimum -25.37, mean -5.757,
maximum 22.16  
Map values for surface "8rx0 R_R SES surface": minimum -22.92, mean -1.509,
maximum 23.73  
To also show corresponding color key, enter the above mlp command and add key
true  

> coulombic #!2.1-9

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
8rx0 A #2.1/A GLU 352  
8rx0 A #2.1/A GLN 353  
8rx0 A #2.1/A LEU 354  
8rx0 A #2.1/A LYS 355  
8rx0 A #2.1/A CYS 356  
8rx0 A #2.1/A CYS 357  
8rx0 A #2.1/A SER 358  
8rx0 A #2.1/A GLY 359  
8rx0 A #2.1/A ILE 360  
8rx0 A #2.1/A LEU 361  
8rx0 A #2.1/A LYS 362  
8rx0 A #2.1/A GLU 363  
8rx0 A #2.1/A MET 364  
8rx0 A #2.1/A PHE 365  
8rx0 A #2.1/A ALA 366  
8rx0 A #2.1/A LYS 367  
8rx0 A #2.1/A LYS 368  
8rx0 A #2.1/A HIS 369  
8rx0 A #2.1/A ALA 370  
8rx0 A #2.1/A ALA 371  
8rx0 A #2.1/A TYR 372  
8rx0 A #2.1/A ALA 373  
8rx0 A #2.1/A TRP 374  
8rx0 A #2.1/A PRO 375  
8rx0 A #2.1/A PHE 376  
8rx0 A #2.1/A TYR 377  
8rx0 A #2.1/A LYS 378  
8rx0 A #2.1/A PRO 379  
8rx0 A #2.1/A VAL 380  
8rx0 A #2.1/A ASP 381  
8rx0 A #2.1/A VAL 382  
8rx0 A #2.1/A GLU 383  
8rx0 A #2.1/A ALA 384  
8rx0 A #2.1/A LEU 385  
8rx0 A #2.1/A GLY 386  
8rx0 A #2.1/A LEU 387  
8rx0 A #2.1/A HIS 388  
8rx0 A #2.1/A ASP 389  
8rx0 A #2.1/A TYR 390  
8rx0 A #2.1/A CYS 391  
8rx0 A #2.1/A ASP 392  
8rx0 A #2.1/A ILE 393  
8rx0 A #2.1/A ILE 394  
8rx0 A #2.1/A LYS 395  
8rx0 A #2.1/A HIS 396  
8rx0 A #2.1/A PRO 397  
8rx0 A #2.1/A MET 398  
8rx0 A #2.1/A ASP 399  
8rx0 A #2.1/A MET 400  
8rx0 A #2.1/A SER 401  
8rx0 A #2.1/A THR 402  
8rx0 A #2.1/A ILE 403  
8rx0 A #2.1/A LYS 404  
8rx0 A #2.1/A ARG 413  
8rx0 A #2.1/A ASP 414  
8rx0 A #2.1/A ALA 415  
8rx0 A #2.1/A GLN 416  
8rx0 A #2.1/A GLU 417  
8rx0 A #2.1/A PHE 418  
8rx0 A #2.1/A GLY 419  
8rx0 A #2.1/A ALA 420  
8rx0 A #2.1/A ASP 421  
8rx0 A #2.1/A VAL 422  
8rx0 A #2.1/A ARG 423  
8rx0 A #2.1/A LEU 424  
8rx0 A #2.1/A MET 425  
8rx0 A #2.1/A PHE 426  
8rx0 A #2.1/A SER 427  
8rx0 A #2.1/A ASN 428  
8rx0 A #2.1/A CYS 429  
8rx0 A #2.1/A TYR 430  
8rx0 A #2.1/A LYS 431  
8rx0 A #2.1/A TYR 432  
8rx0 A #2.1/A ASN 433  
8rx0 A #2.1/A PRO 434  
8rx0 A #2.1/A PRO 435  
8rx0 A #2.1/A ASP 436  
8rx0 A #2.1/A HIS 437  
8rx0 A #2.1/A GLU 438  
8rx0 A #2.1/A VAL 439  
8rx0 A #2.1/A VAL 440  
8rx0 A #2.1/A ALA 441  
8rx0 A #2.1/A MET 442  
8rx0 A #2.1/A ALA 443  
8rx0 A #2.1/A ARG 444  
8rx0 A #2.1/A LYS 445  
8rx0 A #2.1/A LEU 446  
8rx0 A #2.1/A GLN 447  
8rx0 A #2.1/A ASP 448  
8rx0 A #2.1/A VAL 449  
8rx0 A #2.1/A PHE 450  
8rx0 A #2.1/A GLU 451  
8rx0 A #2.1/A MET 452  
8rx0 A #2.1/A ARG 453  
8rx0 A #2.1/A PHE 454  
8rx0 A #2.1/A ALA 455  
8rx0 A #2.1/A LYS 456  
8rx0 N #2.7/N SER 0  
8rx0 N #2.7/N MET 1  
8rx0 N #2.7/N LEU 2  
8rx0 N #2.7/N ILE 3  
8rx0 N #2.7/N LYS 4  
8rx0 N #2.7/N VAL 5  
8rx0 N #2.7/N LYS 6  
8rx0 N #2.7/N THR 7  
8rx0 N #2.7/N LEU 8  
8rx0 N #2.7/N THR 9  
8rx0 N #2.7/N GLY 10  
8rx0 N #2.7/N LYS 11  
8rx0 N #2.7/N GLU 12  
8rx0 N #2.7/N ILE 13  
8rx0 N #2.7/N GLU 14  
8rx0 N #2.7/N ILE 15  
8rx0 N #2.7/N ASP 16  
8rx0 N #2.7/N ILE 17  
8rx0 N #2.7/N GLU 18  
8rx0 N #2.7/N PRO 19  
8rx0 N #2.7/N THR 20  
8rx0 N #2.7/N ASP 21  
8rx0 N #2.7/N LYS 22  
8rx0 N #2.7/N VAL 23  
8rx0 N #2.7/N GLU 24  
8rx0 N #2.7/N ARG 25  
8rx0 N #2.7/N ILE 26  
8rx0 N #2.7/N LYS 27  
8rx0 N #2.7/N GLU 28  
8rx0 N #2.7/N ARG 29  
8rx0 N #2.7/N VAL 30  
8rx0 N #2.7/N GLU 31  
8rx0 N #2.7/N GLU 32  
8rx0 N #2.7/N LYS 33  
8rx0 N #2.7/N GLU 34  
8rx0 N #2.7/N GLY 35  
8rx0 N #2.7/N ILE 36  
8rx0 N #2.7/N PRO 37  
8rx0 N #2.7/N PRO 38  
8rx0 N #2.7/N GLN 39  
8rx0 N #2.7/N GLN 40  
8rx0 N #2.7/N GLN 41  
8rx0 N #2.7/N ARG 42  
8rx0 N #2.7/N LEU 43  
8rx0 N #2.7/N ILE 44  
8rx0 N #2.7/N TYR 45  
8rx0 N #2.7/N SER 46  
8rx0 N #2.7/N GLY 47  
8rx0 N #2.7/N LYS 48  
8rx0 N #2.7/N GLN 49  
8rx0 N #2.7/N MET 50  
8rx0 N #2.7/N ASN 51  
8rx0 N #2.7/N ASP 52  
8rx0 N #2.7/N GLU 53  
8rx0 N #2.7/N LYS 54  
8rx0 N #2.7/N THR 55  
8rx0 N #2.7/N ALA 56  
8rx0 N #2.7/N ALA 57  
8rx0 N #2.7/N ASP 58  
8rx0 N #2.7/N TYR 59  
8rx0 N #2.7/N LYS 60  
8rx0 N #2.7/N ILE 61  
8rx0 N #2.7/N LEU 62  
8rx0 N #2.7/N GLY 63  
8rx0 N #2.7/N GLY 64  
8rx0 N #2.7/N SER 65  
8rx0 N #2.7/N VAL 66  
8rx0 N #2.7/N LEU 67  
8rx0 N #2.7/N HIS 68  
8rx0 N #2.7/N LEU 69  
8rx0 N #2.7/N VAL 70  
8rx0 N #2.7/N LEU 71  
8rx0 N #2.7/N ALA 72  
8rx0 N #2.7/N LEU 73  
8rx0 N #2.7/N ARG 74  
8rx0 N #2.7/N GLY 75  
8rx0 N #2.7/N GLY 76  
8rx0 U #2.9/U LYS 11  
8rx0 U #2.9/U GLU 24  
8rx0 U #2.9/U LYS 33  
8rx0 U #2.9/U LYS 63  
8rx0 U #2.9/U ARG 74  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpgo8m3f9a/ante.in.mol2 -fi mol2 -o /tmp/tmpgo8m3f9a/ante.out.mol2 -fo
mol2 -c bcc -nc -6 -j 5 -s 2 -dr n  
(HIS) ``  
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS) ``  
(HIS) `Info: Finished reading file (/tmp/tmpgo8m3f9a/ante.in.mol2); atoms read
(6), bonds read (4).`  
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS) ``  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS) `Info: Total number of electrons: 48; net charge: -6`  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIS) ``  
Charges for residue HIS determined  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue HIS (net charge -3) with am1-bcc method  
Running ANTECHAMBER command: /usr/lib/ucsf-
chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i
/tmp/tmpct4fbadz/ante.in.mol2 -fi mol2 -o /tmp/tmpct4fbadz/ante.out.mol2 -fo
mol2 -c bcc -nc -6 -j 5 -s 2 -dr n  
(HIS) ``  
(HIS) `Welcome to antechamber 20.0: molecular input file processor.`  
(HIS) ``  
(HIS) `Info: Finished reading file (/tmp/tmpct4fbadz/ante.in.mol2); atoms read
(6), bonds read (4).`  
(HIS) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(HIS) ``  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(HIS) `Info: Total number of electrons: 48; net charge: -6`  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o
sqm.out`  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-
chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1`  
(HIS) ``  
(HIS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(HIS) ``  
Charges for residue HIS determined  
Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 8rx0 A_A SES surface #2.1.2: minimum, -59.32, mean
-28.42, maximum -7.26  
Coulombic values for 8rx0 B_B SES surface #2.2.1: minimum, -12.35, mean 0.68,
maximum 14.69  
Coulombic values for 8rx0 C_C SES surface #2.3.1: minimum, -11.34, mean -0.87,
maximum 8.65  
Coulombic values for 8rx0 D_D SES surface #2.4.1: minimum, -10.87, mean -0.95,
maximum 10.54  
Coulombic values for 8rx0 E_E SES surface #2.5.1: minimum, -14.15, mean -0.34,
maximum 20.31  
Coulombic values for 8rx0 G_G SES surface #2.6.1: minimum, -15.44, mean -1.63,
maximum 11.77  
Coulombic values for 8rx0 N_N SES surface #2.7.1: minimum, -52.31, mean
-24.69, maximum -8.31  
Coulombic values for 8rx0 R_R SES surface #2.8.3: minimum, -12.14, mean -0.33,
maximum 10.71  
Coulombic values for 8rx0 U_U SES surface #2.9.1: minimum, -12.78, mean -1.75,
maximum 7.68  
To also show corresponding color key, enter the above coulombic command and
add key true  

> close #2

> open 8rx0

Summary of feedback from opening 8rx0 fetched from pdb  
---  
warnings | Atom H1 is not in the residue template for MET /B:54  
Atom H1 is not in the residue template for MET /C:1  
Atom H1 is not in the residue template for ALA /D:16  
Atom H1 is not in the residue template for MET /E:1  
  
8rx0 title:  
(NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S,
C223S)-Ub [more info...]  
  
Chain information for 8rx0 #2  
---  
Chain | Description | UniProt  
A | Isoform B of Bromodomain-containing protein 4 | BRD4_HUMAN  
B | von Hippel-Lindau disease tumor suppressor | VHL_HUMAN  
C | Elongin-B | ELOB_HUMAN  
D | Elongin-C | L7N190_MYOLU  
E | Cullin-2 | CUL2_HUMAN  
G | Ubiquitin-conjugating enzyme E2 R1 | UB2R1_HUMAN  
N | NEDD8 | NEDD8_HUMAN  
R | RBX1 |  
U | Ubiquitin | UBC_HUMAN  
  
Non-standard residues in 8rx0 #2  
---  
759 —
(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-
butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-
pyrrolidine-2-carboxamide  
ZN — zinc ion  
  

> hide #!12 models

> hide #!14 models

> hide #!15 models

> hide #!18 models

> hide #!11 models

> fitmap #2 inMap #1.1

Fit molecule 8rx0 (#2) to map cryosparc_P9_J659_007_volume_map_sharp.mrc
(#1.1) using 21370 atoms  
average map value = 0.1073, steps = 68  
shifted from previous position = 0.808  
rotated from previous position = 1.01 degrees  
atoms outside contour = 19127, contour level = 0.26387  
  
Position of 8rx0 (#2) relative to cryosparc_P9_J659_007_volume_map_sharp.mrc
(#1.1) coordinates:  
Matrix rotation and translation  
-0.73092142 0.68081307 0.04740703 197.96935832  
-0.67616473 -0.73184263 0.08489771 441.44230993  
0.09249396 0.02999859 0.99526124 3.71445652  
Axis -0.04040157 -0.03318055 -0.99863245  
Axis point 185.35205193 182.02538297 0.00000000  
Rotation angle (degrees) 137.20181648  
Shift along axis -26.35494835  
  

> show #!2 atoms

> style #!2 stick

Changed 21370 atom styles  

> show #!2 cartoons

> color bfactor #!2

21370 atoms, 1548 residues, atom bfactor range 29 to 137  

> select #2/A & sideonly

441 atoms, 351 bonds, 108 residues, 1 model selected  

> delete sel

> select #2/A:sel349-350

Nothing selected  

> select #2/A:349-350

8 atoms, 7 bonds, 2 residues, 1 model selected  

> delete sel

> select #2/A:457-459,405-412

44 atoms, 42 bonds, 11 residues, 1 model selected  

> delete sel

> show #!2 atoms

> hide #!2 atoms

> show #!2 atoms

> select #2/N & sideonly

297 atoms, 230 bonds, 70 residues, 1 model selected  

> delete sel

Drag select of 7 atoms, 2 residues, 6 bonds  

> delete sel

Drag select of 7 atoms, 2 residues, 5 bonds  

> delete sel

> hide #!2 cartoons

> hide #!2 atoms

> select #2/B

2624 atoms, 2666 bonds, 158 residues, 1 model selected  

> show sel atoms

> show sel cartoons

> select clear

> hide #!1.1 models

> hide #!2 models

> show #!2 models

> show #!1.1 models

> hide #!1.1 models

> show #!1.2 models

> hide #!1.2 models

> select #2/B:195-205 &sideonly

132 atoms, 121 bonds, 11 residues, 1 model selected  

> select #2/B:195-207 &sideonly

149 atoms, 136 bonds, 13 residues, 1 model selected  

> select #2/B:195-209 &sideonly

171 atoms, 157 bonds, 15 residues, 1 model selected  

> delete sel

> show #!1.2 models

> volume #1.2 step 2

> volume #1.2 step 1

> volume #1.1 level 0.1059

> select down

Nothing selected  

> select #2/B:54-60

113 atoms, 113 bonds, 7 residues, 1 model selected  

> delete sel

> volume #1.2 level 0.07721

> ui mousemode right zoom

Drag select of 1.1 cryosparc_P9_J659_007_volume_map_sharp.mrc , 1.2
cryosparc_P9_J659_007_volume_map.mrc , 5 atoms, 1 residues, 5 bonds  

> select clear

> ui mousemode right zoom

> select #2/B

2340 atoms, 2380 bonds, 151 residues, 1 model selected  

> isolde start

> set selectionWidth 4


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

[deleted to fit within ticket limits]



OpenGL version: 3.3.0 NVIDIA 545.23.08
OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: NOVATECH LTD
Model: PC-BX25094
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen Threadripper PRO 3955WX 16-Cores
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           251Gi        34Gi       3.0Gi       761Mi       214Gi       214Gi
	Swap:          2.0Gi       2.0Gi       0.0Ki

Graphics:
	2b:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000]	
	Kernel driver in use: ast

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.19.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.5
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-QScore: 1.0
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
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    h5py: 3.7.0
    html2text: 2020.1.16
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    ihm: 0.33
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    imagesize: 1.4.1
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    msgpack: 1.0.4
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    netCDF4: 1.6.0
    networkx: 2.8.5
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    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
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    pexpect: 4.8.0
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    Pillow: 9.2.0
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    Pygments: 2.12.0
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    PyOpenGL-accelerate: 3.1.5
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    PyQt6-Qt6: 6.3.2
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